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Review
. 2014 Apr 23;114(8):4229-317.
doi: 10.1021/cr4004709. Epub 2014 Jan 29.

Radical S-adenosylmethionine enzymes

Joan B Broderick  1 , Benjamin R Duffus, Kaitlin S Duschene, Eric M Shepard
Affiliations
Review

Radical S-adenosylmethionine enzymes

Joan B Broderick et al. Chem Rev. .
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1
The site-differentiated [4Fe–4S] cluster coordinated by the CX3CX2C radical SAM motif (PDB ID 3IIZ).
Figure 2
Figure 2
The bidentate coordination of S-adenosylmethionine to the unique iron site of the [4Fe–4S] cluster in radical SAM enzymes (PDB ID 3IIZ).
Figure 3
Figure 3
Structures of AdoCbl (left) and SAM (right).
Figure 4
Figure 4
Reductive cleavage of S-3′,4′-anhydroadenosyl-l-methionine (anSAM) results in generation of the stable allylic radical species 5′-deoxy-3′,4′-anhydroadenosine-5′-yl (anAdo•).
Figure 5
Figure 5
The cleavage of SAM to generate methionine and the dAdo• is a reductive cleavage event, requiring the input of one electron.
Figure 6
Figure 6
X-band EPR spectra of photoreduced PFL-AE before (A) and after addition of PFL (B), photoreduction time indicated in minutes. (C) Spin quantitation of the EPR spectra in (A) for the amount of the [4Fe–4S]+ cluster (+) and EPR spectra in (B) for the amount of glycyl radical (■) as a function of illumination time. Reprinted with permission from ref (21). Copyright 2000 American Chemical Society.
Figure 7
Figure 7
Framework mechanism for radical SAM cleavage (PDB ID 3IIZ).
Figure 8
Figure 8
Reduction potentials for SAM and the [4Fe–4S] cluster based on experimental measurements for LAM.
Figure 9
Figure 9
Regioselective cleavage of the S–C bonds of SAM. Bonds that may undergo enzymatic-based homolytic cleavage are demarked in varying colors with S–C(5′) in blue, S–C(γ) in red, and the S–C(methyl) in magenta.
Figure 10
Figure 10
The reductive cleavage of SAM occurs through an inner-sphere mechanism involving a direct path between the unique iron ion of the cluster and the sulfonium group antibonding S–C(5′) orbital.
Figure 11
Figure 11
Illustration of the results of the LAM ENDOR studies using stabilized substrate and product radical analogue intermediates (PDB ID 2A5H). In all cases, van der Waals contacts are maintained between the 5′-methyl of dAdoH (carbons shown in gray) and the substrate/product radicals. Illustrations for the substrate radicals generated upon reaction with trans-4,5-dehydro- l-lysine (DHLys, left), 4-thia-l-lysine (SLys, middle), and the product radical generated upon equilibration of the reduced state of the enzyme with SAM and l-α-lysine (right). Adapted with permission from ref (38). Copyright 2006 American Chemical Society.
Figure 12
Figure 12
Example of a radical SAM partial TIM barrel structure (PDB ID 3CB8 for PFL-AE). N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, and SAM in green sticks.
Figure 13
Figure 13
Homolytic cleavage of the Co–C bond to generate cob(II)alamin and the 5′- deoxyadenosyl radical.
Figure 14
Figure 14
PFL-AE reaction scheme catalyzing the activation of PFL by stereospecific (pro-S) hydrogen atom abstraction from PFL G734 (in E. coli).
Figure 15
Figure 15
Left: Mössbauer spectra of 56Fe PFL-AE reconstituted with 57Fe for incorporation into the unique iron site in the absence (A) and presence (B) of SAM. The solid line in (A) is the experimental spectrum of [4Fe–4S]2+ clusters in PFL-AE normalized to 70% of the total Fe absorption of (A). The solid line in (B) is the spectrum of the control sample containing only the reconstitution ingredients and SAM but without PFL-AE and is normalized to 15% of the total Fe absorption of (B). A difference spectrum of (B) minus (A) is shown in (C). Spectrum (D) is a difference spectrum of the samples (A) and (B) recorded in a parallel field of 8 T. Reprinted with permission from ref (93a). Copyright 2002 American chemical Society. Right: Illustration of the PFL-AE [4Fe–4S] cluster with 57Fe (purple sphere) in the unique site bound by SAM, with the other sites occupied by natural abundance iron (56Fe, green spheres) (PDB ID 3CB8).
Figure 16
Figure 16
35-GHz pulsed ENDOR spectra of PFL-AE with 17O (A) and 13C (B) carboxylato-labeled and 15N-amino-labeled (C) SAM as compared to data from an unlabeled sample, at g⊥. Reprinted with permission from ref (67). Copyright 2005 American Chemical Society.
Figure 17
Figure 17
Representative valence delocalization of biological [4Fe–4S]2+ clusters containing two Fe2.5+–Fe2.5+ pairs (left, top and bottom). Representative valence localization of [4Fe–4S]2+ clusters in PFL-AE isolated from whole cells containing one Fe2.5+–Fe2.5+ pair and one Fe3+–Fe2+ pair (right, top and bottom) (PDB ID 3CB8).
Figure 18
Figure 18
PFL-AE crystal structure (PDB ID 3CB8). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, SAM in green sticks, 7-mer peptide in dark gray sticks. Right: Active site of PFL-AE where [4Fe–4S] cluster (yellow and rust), SAM (green carbons), and 7-mer peptide (gray carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating cluster are depicted in lines.
Figure 19
Figure 19
Docking model of PFL-AE (PDB ID 3CB8). Best dock as produced by ZDOCK, with Cα of G734 in spacefill and radical domain of PFL (residues 712–759) in magenta. PFL-AE helices in cyan, strands in yellow, and loops in gray. The [4Fe–4S] cluster (yellow and rust) and SAM (green carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Reprinted with permission from ref (29). Copyright 2008 National Academy of Sciences.
Figure 20
Figure 20
Schematic representation of PFL: left, crystal structure of closed conformation (PDB ID 2PFL); and right, model for the open conformation. Radical domain shown in red where Gly734 is a red sphere and active site residues Cys418 and Cys419 are yellow spheres. Reprinted with permission from ref (149). Copyright 2010 American Society for Biochemistry and Molecular Biology.
Figure 21
Figure 21
The X-ray crystal structures of the activating enzyme substrates from left to right: GD, PFL, and aRNR (PDB IDs: 1R8W, 2PFL, and 1HK8, respectively). All structures possess a core 10-stranded β-barrel motif assembled in a manner antiparallel to two parallel five-stranded β-sheets. The β-barrel core is surrounded by α-helices forming the β/α-barrel. Radical domains, highlighted in magenta, for GD, PFL, and aRNR are composed of the amino acids 731–782, 702–754, and 540–586 (where aRNR possesses a mostly disordered C-terminal domain), respectively.
Figure 22
Figure 22
The conversion of dethiobiotin to biotin catalyzed by biotin synthase (BioB).
Figure 23
Figure 23
Reduction of BioB containing [2Fe–2S]2+ clusters. (A) UV/visible spectra of BioB were recorded as the cell potential was lowered by titration with dithionite. (Inset) Difference spectra associated with the first wave of reduction (solid curve) and the second wave of reduction (dashed curve) having maxima at 460 nm. (B) The absorbance change at 452 nm was followed as a function of the measured cell potential. Reprinted with permission from ref (24a). Copyright 2001 American Chemical Society.
Figure 24
Figure 24
UV–visible spectrum of BioB under assay conditions reveals features characteristic of both [4Fe–4S]2+ and [2Fe–2S]2+ clusters. Reprinted with permission from ref (24a). Copyright 2001 American Chemical Society.
Figure 25
Figure 25
BioB crystal structure (PDB ID 1R30). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] and [2Fe–2S] clusters in yellow and rust spheres, SAM in green sticks, dethiobiotin in dark gray sticks. Right: Active site of BioB where [4Fe–4S] and [2Fe–2S] clusters (yellow and rust), SAM (green carbons), and dethiobiotin (gray carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 26
Figure 26
The mechanism of biotin formation from dethiobiotin as catalyzed by BioB.
Figure 27
Figure 27
LipA reaction scheme catalyzing the conversion of octanoyl-acyl carrier protein to lipoyl-acyl carrier protein.
Figure 28
Figure 28
The mechanism of lipoyl-acyl carrier protein from octanoyl-acyl carrier protein as catalyzed by LipA.
Figure 29
Figure 29
LAM reaction scheme catalyzing the conversion of l-α-lysine to l-β-lysine.
Figure 30
Figure 30
LAM crystal structure (PDB ID 2A5H). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, SAM in green sticks, PLP in dark gray sticks. Right: Active site of LAM where [4Fe–4S] cluster (yellow and rust), SAM (green carbons), and PLP (gray carbons) are depicted in sticks with oxygens colored red, nitrogens colored blue, and phosphorus in orange. The cysteine residues (light blue carbons) involved in ligating cluster are depicted in lines.
Figure 31
Figure 31
The conversion of l-α-lysine to l-β-lysine as catalyzed by lysine 2,3-aminomutase.
Figure 32
Figure 32
The synthesis of 3-methyl-d-ornithine from l-α-lysine as catalyzed by PylB in the first step of pyrrolysine biosynthesis.
Figure 33
Figure 33
PylB crystal structure (PDB ID 3T7V). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, SAM in green sticks, methylornithine in dark gray sticks. Right: Active site of PylB where [4Fe–4S] cluster (yellow and rust), SAM (green carbons), and methylornithine (gray carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating cluster are depicted in lines.
Figure 34
Figure 34
The molybdopterin cofactor (Moco) is composed of a molybdenum ion coordinated by a low molecular weight tricyclic pterin ligand via dithiolene coordination.
Figure 35
Figure 35
The observed rearrangement of carbon atoms in the MoaA/MoaC reaction.
Figure 36
Figure 36
MoaA crystal structure (PDB ID 2FB3). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] clusters in yellow and rust spheres, dAdoH and Met in green sticks, GTP in dark gray sticks. Right: Active site of MoaA where [4Fe–4S] cluster (yellow and rust), dAdoH and Met (green carbons), and GTP (gray carbons) are depicted in sticks with oxygens colored red, nitrogens colored blue, and phosphates in orange. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 37
Figure 37
Top panel: 15N ENDOR evidence of 5′-GTP interaction with C-terminal [4Fe–4S], using 14N and 15N 5′-GTP substrate and C24S/C28S/C31S MoaA. Bottom panel: Comparison of 14N ENDOR of substrate analogue 5′-ITP with 5′-GTP that have equivalent 14N hyperfine interaction with the C-terminal [4Fe–4S] cluster. Reprinted with permission from ref (38). Copyright 2006 American Chemical Society.
Figure 38
Figure 38
Proposed specific transformations that are catalyzed by enzymes MoaA and MoaC.
Figure 39
Figure 39
Proposed mechanism of formation of 3′,8-cH2GTP by radical SAM enzyme MoaA.
Figure 40
Figure 40
The biosynthesis of thiamine pyrophosphate. 4-Amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate (HMP-PP) (left) is ultimately coupled with 4-methyl-5-(β-hydroxyethyl)thiazole phosphate carboxylate (thiazole-P carboxylate) (right) to form thiamine pyrophosphate. The radical SAM enzymes ThiC and ThiH are highlighted in red. The generation of dehydroglycine differs between aerobes and anaerobes, which is highlighted as well.
Figure 41
Figure 41
Carbon and nitrogen isotopic label studies in the ThiC conversion of AIR to HMP-P. All carbon and nitrogen atoms originate from AIR, and the two carbon atoms (from the C-1′ and C-3′ positions) not incorporated into HMP-P produce formic acid and carbon monoxide, respectively.
Figure 42
Figure 42
ThiC crystal structure (PDB ID 3EPO). N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, HMP-P in dark gray sticks.
Figure 43
Figure 43
Reaction of the heterocyclic rearrangement catalyzed by radical SAM enzyme QueE.
Figure 44
Figure 44
Proposed mechanism in the QueE heterocyclic rearrangement.
Figure 45
Figure 45
F0 synthase reaction catalyzed by bifunctional enzyme FbiC. The monofunctional units of FbiC can be isolated separately and, in vitro, catalyze the same reaction, with tyrosine and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to make the 8-hydroxy-7-desmethyl-5-deazariboflavin chromophore F0.
Figure 46
Figure 46
Proposed mechanism of radical initiation and probable involvement of CofH. Tyrosine homolytic Cα–Cβ bond cleavage products are depicted in black, while heterolytic bond cleavage products are depicted in aqua.
Figure 47
Figure 47
Transformation catalyzed by radical SAM enzyme MqnC.
Figure 48
Figure 48
Ring cyclization mechanism catalyzed by radical SAM enzyme MqnC.
Figure 49
Figure 49
Transformation catalyzed by radical SAM enzyme MqnE.
Figure 50
Figure 50
Mechanism of dAdo• addition to a vinylic ether double bond, catalyzed by radical SAM enzyme MqnE.
Figure 51
Figure 51
Structure homology model of the amino acid sequence of MqnE (T. thermophilus) (blue), aligned to the HydE crystal structure (PDB ID 3CIX) (pink) (section 12.2.5.2). Radical SAM motif is colored in yellow, cysteines involved in ligating the [4Fe–4S] are shown as yellow sticks, while the [4Fe–4S] cluster is depicted as yellow and rust sticks. For clarity, the [2Fe–2S] cluster of HydE has been omitted. MqnE structural model was generated using the protein structure prediction server Phyre2, where the HydE template model yielded the top hit.
Figure 52
Figure 52
Radical fragmentation–recombination reaction catalyzed by radical SAM enzymes NosL and NocL.
Figure 53
Figure 53
Proposed fragmentation–recombination mechanism in the conversion of l-Trp to MIA catalyzed by NosL and NocL.
Figure 54
Figure 54
Representative radical SAM methyltransferase enzymes (RMSTs). Enzymes are organized by their class, which are differentiated by the top panel. Members of each class are differentiated by the type of methyl transfer catalyzed.
Figure 55
Figure 55
The modification of adenosine 2503 in 23S RNA of the bacterial large ribosomal subunit via methylation of the C2 or C8 position as catalyzed by RlmN or Cfr (two representative members of the class A RSMTs), respectively. The proposed mechanism for methylation of C2 by RlmN is depicted along the left side as shown using green arrows. The proposed mechanism for methylation of C8 by Cfr is depicted along the right side as shown using magenta arrows.
Figure 56
Figure 56
RlmN crystal structure (PDB ID 3RFA). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, and SAM in green sticks. Right: Active site of RlmN where [4Fe–4S] cluster (yellow and rust) and SAM (green carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating cluster are depicted in lines.
Figure 57
Figure 57
Proposed reaction scheme for class B RSMTs.
Figure 58
Figure 58
PhpK reaction scheme catalyzing the conversion of N-acetyldemethylphosphinothricin, NAcDMPT, to N-acetylphosphinothricin, NAcPT.
Figure 59
Figure 59
TsrM reaction scheme catalyzing the conversion of tryptophan to 2-methyltrytophan.
Figure 60
Figure 60
GenK reaction scheme catalyzing the conversion of Gentamicin X2 to G418.
Figure 61
Figure 61
HpnP reaction scheme catalyzing the methylation of the C2 position in bacterial hopanoids. A few representative hopanoids are shown here.
Figure 62
Figure 62
YtkT reaction scheme catalyzing the methylation of a yatakemycin (YTM) intermediate prior to cyclopropane ring formation.
Figure 63
Figure 63
Methylthiolations of nucleic acid and protein residues. Left: Methylthiolations as catalyzed by MiaB (E. coli and T. maritima) and YmcB (B. subtilis) where the tRNA adenosine base is modified from i6A (when X = H) to ms2i6A (when X = SCH3). Middle: Methylthiolations as catalyzed by YqeV (B. subtilis) and CDKAL1 (mammalian tRNALys UUU) where the tRNA adenosine base is modified from t6A (when Y = H) to ms2t6A (when Y = SCH3). Right: Methylthiolation as catalyzed by RimO (E. coli ribosomal S12) where Asp89 (when Z = H) is modified to β-methylthio Asp89 (when Z = SCH3).
Figure 64
Figure 64
RimO crystal structure (PDB ID 4JC0). Left: N-terminal UPF0004 domain colored in light orange, radical SAM domain in light blue, C-terminal TRAM domain in light pink, [4Fe–4S] clusters in yellow and rust spheres, and SAM in green sticks. Right: Active site of RimO where the [4Fe–4S] clusters (yellow and rust) and pentasulfide moiety (yellow) are depicted in sticks. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 65
Figure 65
Proposed RimO mechanism catalyzing the methylthiolation of Asp89 of the ribosomal S12 protein.
Figure 66
Figure 66
Mechanism of formylglycine generation for cysteine (anSMEcpe) and serine type (AtsB/anSMEkp) sulfatase maturating enzymes. The order of H-atom abstraction and proton abstraction events has not yet been established.
Figure 67
Figure 67
anSME crystal structure (PDB ID 4K39). Left: N-terminal/radical SAM domain colored in light blue, SPASM domain in light pink, remaining two α-helices in light green, [4Fe–4S] clusters in yellow and rust spheres, SAM in green, and peptide in gray sticks. Right: Active site of anSME where the [4Fe–4S] clusters (yellow and rust), SAM (green carbons), and peptide (gray carbons) depicted in sticks with oxygens colored red and nitrogens colored blue. D277 (magenta carbons, depicted in sticks) has been identified as the catalytic base (see Figure 66). Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 68
Figure 68
The dehydrogenation reaction catalyzed by BtrN during butirosin biosynthesis. The order of H-atom abstraction and proton abstraction events has not yet been definitively established, and along these lines it has only recently been suggested that formation of the α-hydroxyalkyl radical by H-atom abstraction may activate the C3-hydroxyl functional group by decreasing its pKa. Goldman et al. have identified the putative base involved in catalysis as being Arg152.
Figure 69
Figure 69
BtrN crystal structure (PDB ID 4M7T). Left: Radical SAM domain colored in light blue, C-terminal domain in light pink, linker regions in light green, [4Fe–4S] clusters in yellow and rust spheres, SAM in green, and DOIA in gray sticks. Right: Active site of BtrN where the [4Fe–4S] clusters (yellow and rust), SAM (green carbons), and DOIA (gray carbons) depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 70
Figure 70
Involvement of radical SAM enzyme PqqE in pyrroloquinoline quinone (PQQ) biosynthesis. PqqE is proposed to be involved in the condensation of peptide residues Glu and Tyr, but its specific substrate is unknown.
Figure 71
Figure 71
The biosynthesis of yW. G at position 37 is transformed to imG-14 through the actions of TRM5 and TYW1, which is subsequently converted to yW through the actions of TYW2, TYW3, and TYW4.
Figure 72
Figure 72
phTYW1 crystal structure (PDB ID 2YX0). N-terminal domain colored in wheat, radical SAM domain in light blue, and C-term domain in light pink.
Figure 73
Figure 73
Proposed mechanism for the conversion of N-methylguanosine (m1G) to 4-demethylwyosine (img-14) catalyzed by TYW1.
Figure 74
Figure 74
Solution NMR structure of Subtilosin A (PDB ID 1PXQ).
Figure 75
Figure 75
Proposed hydrogen atom abstraction mechanism in thioether bond formation observed for radical SAM enzymes AlbA and SkfB.
Figure 76
Figure 76
Thuricin CD, like subtilosin A, contains three thioether cross-links between cysteine residues and the α-carbons of the modified amino acids, which are two threonines and a serine in Trnα and one tyrosine, one alanine, and one threonine in Trnβ.
Figure 77
Figure 77
Structure of sporulation killing factor (SKF). The thioether bond is highlighted in blue, while the cysteine disulfide bond is highlighted in red.
Figure 78
Figure 78
The mechanism of Cα–Cβ tyrosine bond cleavage as catalyzed by ThiH. Bond breakage may either occur through a heterolytic process forming dehydroglycine directly or through a homolytic process forming a glycyl radical.
Figure 79
Figure 79
SPL reaction scheme catalyzing the conversion of SP to TpT.
Figure 80
Figure 80
Depiction of the two possible spore photoproducts with either 5R or 5S configuration.
Figure 81
Figure 81
SPL crystal structure (PDB ID 4FHD). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, and SAM in green sticks. Right: Active site of SPL where [4Fe–4S] cluster (yellow and rust) and SAM (green carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating cluster are depicted in lines.
Figure 82
Figure 82
Proposed mechanism for the repair of SP as catalyzed by SPL.
Figure 83
Figure 83
Natural products d-desosamine and methymycin. Radical SAM enzyme DesII is involved in the biosynthesis of d-desosamine.
Figure 84
Figure 84
Radical SAM enzyme DesII catalyzes a redox-neutral deamination (top reaction), as well as an oxidative dehydrogenation (bottom reaction).
Figure 85
Figure 85
Proposed mechanism in DesII-catalyzed deamination. Depicted in blue is an ethanolamine ammonia lyase-inspired mechanism involving the formation of a carbinolamine intermediate. Depicted in red is an E1cb-type mechanism involving a stabilized enol radical. Double black full arrows represent product leaving the active site, substrate coordination, and dAdo• generation.
Figure 86
Figure 86
Proposed mechanism of DesII-catalyzed oxidative dehydrogenation. Note that electron transfer is proposed to occur from the product radical back to the oxidized [4Fe–4S]2+ cluster, as redox cycling of the FeS cluster has been demonstrated.
Figure 87
Figure 87
C–P bond cleavage of methylphosphonate by radical SAM enzyme PhnJ.
Figure 88
Figure 88
Mechanism of C–P bond cleavage catalyzed by radical SAM enzyme PhnJ.
Figure 89
Figure 89
Hypothetical mechanism for the Elp3-catalyzed demethylation of DNA. An alternative pathway has been proposed, which could account for product formation in the absence of an external nucleophile; see Wu and Zhang.
Figure 90
Figure 90
Oxygen-independent biosynthetic pathway of heme and heme d1 from uroproporphyrinogen III. Biosynthetic involvement of radical SAM enzymes and the transformation catalyzed is bolded in red, while nonradical SAM enzyme transformations are bolded in blue. Pathway-dependent transformations that do not strictly require radical SAM enzyme involvement are highlighted in purple.
Figure 91
Figure 91
HemN crystal structure (PDB ID 1OLT). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] cluster in yellow and rust spheres, and SAM in green sticks. Right: Active site of HemN where the [4Fe–4S] cluster (yellow and rust) and SAM (green carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 92
Figure 92
The mechanism of iterative decarboxylation events by HemN.
Figure 93
Figure 93
Chlorophyll and bacteriochlorophyll biosynthetic pathway. Involvement of radical SAM enzymes (and their respective transformation catalyzed) is bolded in red, while nonradical SAM enzyme involvement is bolded in blue.
Figure 94
Figure 94
Putative mechanism of BchE-catalyzed ring cyclization, where both the radical SAM Fe–S cluster and the cobalamin-binding domains participate in the ring cyclization reaction.
Figure 95
Figure 95
Nitrogenase FeMo-cofactor assembly.
Figure 96
Figure 96
Radical SAM-based carbide insertion during FeMo-co biosynthesis. NifB is proposed to form the [Fe8–S9] L-cluster from the K-cluster, two [4Fe–4S] precursor units. The left pathway invokes methylation of a cluster sulfide followed by generation of a methylene radical upon hydrogen atom abstraction by the dAdo•. The right pathway proposes methyl radical formation via SAM cleavage followed by addition to an Fe ion of the cluster where further processing to a methylene radical occurs.
Figure 97
Figure 97
The proposed maturation pathway for the biosynthesis of the [FeFe]-hydrogenase H-cluster.
Figure 98
Figure 98
The mechanism of diatomic ligand biosynthesis as catalyzed by HydG. Cα–Cβ tyrosine bond cleavage has recently been demonstrated to occur through a heterolytic process (see text)., Formation of the diatomics requires in some capacity the presence of the C-terminal [4Fe–4S] cluster where dehydroglycine is further processed into CN– and CO; the in vitro complexation/trapping of these diatomics are illustrated at the bottom. Bottom right reprinted with permission from ref (78b). Copyright 2010 American Chemical Society.
Figure 99
Figure 99
HydE crystal structure (PDB ID 3IIZ). Left: N-terminal domain colored in wheat, radical SAM domain in light blue, C-terminal domain in light pink, [4Fe–4S] and [2Fe–2S] clusters in yellow and rust spheres, and SAM in green sticks. Right: Active site of HydE where the [4Fe–4S] and [2Fe–2S] clusters (yellow and rust) and SAM (green carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 100
Figure 100
The iron-guanylylpyridinol cofactor (FeGP-co) of [Fe]-hydrogenase.
Figure 101
Figure 101
Structure homology model of the amino acid sequence of HcgA (M. maripaludis) (green), aligned to the HydE crystal structure (PDB ID 3CIX) (pink) (section 12.2.5.2). Radical SAM motif is colored in yellow, cysteines involved in ligating the [4Fe–4S] are shown as yellow sticks, while the [4Fe–4S] cluster is depicted as yellow and rust sticks. For clarity, the [2Fe–2S] cluster of HydE has been omitted. MqnE structural model was generated using the protein structure prediction server Phyre2, where the HydE template model yielded the top hit.
Figure 102
Figure 102
Proposed AviX12 reaction catalyzing the epimerization reaction to convert gavibamycin N1 to avilamycin A.
Figure 103
Figure 103
Dph2 crystal structure (PDB ID 3LZD). Left: Domain 1 colored in wheat, domain 2 in light blue, domain 3 in light pink, C-terminal domain in light green, and [4Fe–4S] cluster in yellow and rust spheres. Right: Active site of Dph2 where the [4Fe–4S] cluster (yellow and rust) is depicted in sticks. Cysteines (light blue carbons) involved in ligating clusters are depicted in lines.
Figure 104
Figure 104
Proposed reaction mechanism for Dph2 catalyzing the modification of EF2-His600 during the first step of dipthamide biosynthesis.
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