Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2002 Apr;11(4):723-38.
doi: 10.1110/ps.4570102.

Structural genomics: a pipeline for providing structures for the biologist

Mark R Chance  1 , Anne R Bresnick, Stephen K Burley, Jian-Sheng Jiang, Christopher D Lima, Andrej Sali, Steven C Almo, Jeffrey B Bonanno, John A Buglino, Simon Boulton, Hua Chen, Narayanan Eswar, Guoshun He, Raymond Huang, Valentin Ilyin, Linda McMahan, Ursula Pieper, Soumya Ray, Marc Vidal, Li Kai Wang
Affiliations
Review

Structural genomics: a pipeline for providing structures for the biologist

Mark R Chance et al. Protein Sci. 2002 Apr.
No abstract available

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Modeling target sequences based on a template structure (Marti-Renom et al. 2000).
Fig. 2.
Fig. 2.
Ribbon diagram of E. coli Gab. (A) Oligomeric architecture of the Gab tetramer. Monomers are colored yellow, blue, gold, and green. The N terminus is labeled N for each protomer. Large magenta spheres mark the Fe(II) ion in each protomer. Each active site is well separated and distinct. Oligomeric interactions are mediated primarily between α1–3 and α5–6 between respective protomers. (B) Protomer of the Gab protein. N- and C-terminal residues are denoted with an N and C, respectively. Secondary structural elements are denoted α1–7 and β1–16 corresponding to the sequence alignment presented in Fig. 3 ▶. Active site Fe(II) and residues His 160, Asp 162, His 292, and Arg 305 are labeled. Graphics prepared using SETOR (Evans 1993).
Fig. 2.
Fig. 2.
Ribbon diagram of E. coli Gab. (A) Oligomeric architecture of the Gab tetramer. Monomers are colored yellow, blue, gold, and green. The N terminus is labeled N for each protomer. Large magenta spheres mark the Fe(II) ion in each protomer. Each active site is well separated and distinct. Oligomeric interactions are mediated primarily between α1–3 and α5–6 between respective protomers. (B) Protomer of the Gab protein. N- and C-terminal residues are denoted with an N and C, respectively. Secondary structural elements are denoted α1–7 and β1–16 corresponding to the sequence alignment presented in Fig. 3 ▶. Active site Fe(II) and residues His 160, Asp 162, His 292, and Arg 305 are labeled. Graphics prepared using SETOR (Evans 1993).
Fig. 3.
Fig. 3.
Structure-based sequence alignment for Gab with other non-haem iron oxygenases. Structure-based sequence alignment produced by PrISM (Yang and Honig 1999). 1JR7, 1drt, 1dcs, and 1bk0 represent PDB codes for E. coli Gab, clavaminate synthase 1 (CAS), deacetoxycephalosporin C synthase (DOACS), and isopenicillin N synthase (IPNS), respectively. Highlighted residues in alignment are color-coded blue (active site residues) and magenta if conserved across all family members, yellow if conserved between DOACS and IPNS, and orange if conserved between CAS and Gab. Sequence identities in the structure-based alignment revealed 15.6% identity between Gab and CAS, 10.3% identity between Gab and DOACS, 5.0% identity between Gab and IPNS; 18.3% sequence identity was found between DOACS and IPNS, 7.4% identity between DOACS and CAS, and 9.8% identity between CAS and IPNS. Secondary structural elements (above) and sequence numbering (below) are shown for E. coli Gab in the alignment.
Fig. 4.
Fig. 4.
The flowchart of Automated Structure Determination Platform.
Fig. 5.
Fig. 5.
(A) P097 is a three-layer α-β-α sandwich. β Strands are painted as cyan, α helices are painted as red, and loops are painted as gray. (B) P097 forms a tightly packed dimer. Large red spheres represent putative metal ions.
Fig. 5.
Fig. 5.
(A) P097 is a three-layer α-β-α sandwich. β Strands are painted as cyan, α helices are painted as red, and loops are painted as gray. (B) P097 forms a tightly packed dimer. Large red spheres represent putative metal ions.
Fig. 6.
Fig. 6.
Multiple alignments of 16 sequences with at least 30% identity to P097 from the Swiss-Prot database revealed several conserved regions (A,B). (red) Completely conserved residues; (white) nonconserved residues. (A) The P097 monomer. Conserved residues at the dimer interface are revealed as a red patch on the righthand side of the molecule. (B) The surface of the P097 dimer. The two putative metal ions are represented by blue spheres and may indicate important ligand binding sites as indicated by the conserved residues around the putative metal binding site. Conserved residues at the dimer interface are completely buried.
Fig. 6.
Fig. 6.
Multiple alignments of 16 sequences with at least 30% identity to P097 from the Swiss-Prot database revealed several conserved regions (A,B). (red) Completely conserved residues; (white) nonconserved residues. (A) The P097 monomer. Conserved residues at the dimer interface are revealed as a red patch on the righthand side of the molecule. (B) The surface of the P097 dimer. The two putative metal ions are represented by blue spheres and may indicate important ligand binding sites as indicated by the conserved residues around the putative metal binding site. Conserved residues at the dimer interface are completely buried.
See this image and copyright information in PMC

References

    1. Abrahams, J.P. and Leslie, A.G.W. 1996. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D52 30–42. - PubMed
    1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. - PMC - PubMed
    1. Baker, D. and Sali, A. 2001. Protein structure prediction and structural genomics. Science 5 93–96. - PubMed
    1. Baldwin, J.E. and Abraham, E. 1988. Biosynthesis of penicillins and cephalosporins. Nat. Prod. Rep. 5 129–145. - PubMed
    1. Bonnano, J.B., Edo, C., Eswar, N., Pieper, U., Romanowski, M.J., Ilyin, V.A., Gerchman, S.E., Kycia, H., Studier, F.W., Sali, A., and Burley, S.K. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc. Natl. Acad. Sci. 98 12896–12901. - PMC - PubMed

Publication types

Associated data

LinkOut - more resources