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
. 2003;53 Suppl 6(Suppl 6):340-51.
doi: 10.1002/prot.10555.

CASP5 target classification

Affiliations

CASP5 target classification

Lisa N Kinch et al. Proteins. 2003.

Abstract

This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was "natively unfolded"; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
CASP5 domains. Thumbnail images of CASP5 targets, created by using the graphics program RasMol. Models of the CASP5 target structures are split into domains, and indicated domains are colored according to secondary structural elements: α-helix (pink) and β-sheet (yellow), with the remaining secondary structural elements colored gray. The number to the lower left of each image indicates the target length, and colored block to the upper left of each image indicates the target classification: CM (red), CM/FR(H) (pink), FR(H) (blue), FR(A) (cyan), FR(A)/NF (green), and NF (black).
Fig. 2
Fig. 2
Target T0149: domains cross-classification categories. A: A molscript rendering of the two domains of target T0149 (E. coli hypothetical protein yjiA). The N-terminal domain is colored in white, and the C-terminal domain is colored in gray. The N-terminal domain (T0149_1) is homologous to (B), the Nitrogenase iron protein from C. pasteurianum (1cp2) and was assigned as CM/FR(H), whereas the C-terminal domain (T0149_2) was assigned to a new fold, although it displayed some topological similarity to (C) the histidine-containing phosphocarrier protein (1pch).
Fig. 3
Fig. 3
Classification of comparative modeling targets: similarity to templates. The numbers of domains that have similarity scores (Sseq) within the indicated bin ranges (x axis) are depicted as closed circles. A smoothed line connects the circles to illustrate the resulting bimodal distribution of the comparative modeling target domains.
Fig. 4
Fig. 4
Identification of distant structure analogs using vector search. A: The experimental model structure of the first domain (T0187_1) of a putative glycerate kinase from T. maritima found B a structural analog cobalt precorrin-4methyltransferase CbiF domain 2 (1cbf) using a vector search program. C: The first model prediction of one group (Brooks, Group 373) is based on this parent template. D: Another CASP5 target domain (T0149_2) was linked to T0187_1 by using a different definition of core secondary structural elements (includes the purple strand). The vector search program identified (E) homoserine dehydrogenase domain 2 (1ebf_B149-337) and (F) heat shock protein HSP90 (1a4h_A1-214) as distant structural analogs of target T0149_2. Secondary structural elements belonging to the core fold are colored according to type: β-sheets are yellow and α-helices are blue. The β-strand colored in purple represents a core element in target T0149_2 and related structures. The β-strand colored green is deleted in target T0149_2 and related structures. Secondary structural elements that are treated as insertions are colored white.

Similar articles

Cited by

References

    1. Schlessman JL, Woo D, Joshua-Tor L, Howard JB, Rees DC. Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. J Mol Biol. 1998;280:669–685. - PubMed
    1. Herzberg O, Reddy P, Sutrina S, Saier MH, Jr, Reizer J, Kapadia G. Structure of the histidine-containing phosphocarrier protein HPr from Bacillus subtilis at 2.0-A resolution. Proc Natl Acad Sci USA. 1992;89:2499–2503. - PMC - PubMed
    1. van den Akker F. Structural insights into the ligand binding domains of membrane bound guanylyl cyclases and natriuretic peptide receptors. J Mol Biol. 2001;311:923–937. - PubMed
    1. Hickman AB, Namboodiri MA, Klein DC, Dyda F. The structural basis of ordered substrate binding by serotonin N-acetyltransferase: enzyme complex at 1.8 A resolution with a bisubstrate analog. Cell. 1999;97:361–369. - PubMed
    1. Angus-Hill ML, Dutnall RN, Tafrov ST, Sternglanz R, Ramakrishnan V. Crystal structure of the histone acetyltransferase Hpa2: a tetrameric member of the Gcn5-related N-acetyltransferase superfamily. J Mol Biol. 1999;294:1311–1325. - PubMed

LinkOut - more resources