The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

These structures provide support for a hypothesis that explains the in vivo action of LuxS. Specifically, acting as a homodimer, the protein binds a methionine analog, S-ribosylhomocysteine (SRH). The zinc atom is in position to cleave the ribose ring in a step along the synthesis pathway of AI-2.

OBJECTIVE: Following several reports of linkage of obesity related phenotypes to human chromosome 20q we sought to determine whether variations of the melanocortin 3 receptor (MC3R) gene are associated with obesity. DESIGN: We screened the MC3R gene coding region and approximately 2 kb of 5 H and 3 H¯a nking sequences for DNA variants in unrelated extremely obese women and average weight controls using polymerase chain reaction (PCR) single strand conformation polymorphism (SSCP) analysis and DNA sequencing. SUBJECTS: 124 unrelated extremely obese women (body mass index, (BMI) ! 40 kgam 2 ) and 85 average weight controls (BMI`27 kgam 2 ). MEASUREMENTS: Radiation hybrid (RH) mapping was performed to localize the MC3R gene. 5 H and 3 H¯a nking sequences of MC3R gene were cloned. PCR-SSCP and DNA sequencing were used to detect mutations in the MC3R gene coding region and¯anking sequences. RESULTS: RH mapping localized the MC3R gene to 20q13, between markers D20S100 and D20S149. 1083 bp 5 H and 653 bp 3 H¯a nking region of the MC3R gene were cloned. A missense mutation ( 241, codon 81 ATTaGTT, Ile 3 Val) was found in the MC3R coding region. Four more variants were detected in the 5 H¯a nking sequence: À201(C 3 G), À239 (A 3 G), À762(A 3 T) and À769(T 3 C). Compared with controls, no signi®cant allele frequency differences were found. Racial differences were found for the 241, À201, À239 and À762 polymorphisms. CONCLUSIONS: Several sequence variants were found in the MC3R gene coding region and in 5 H¯a nking sequences. However, none of the variants were associated with obesity phenotypes. The linkage of extreme human obesity on 20q13 is likely caused by genes other than MC3R.

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We have begun a small scale structural genomics project aimed at obtaining fold information for the set of sequence families comprising eukaryotic intracellular signaling domains, and exploiting that information to understand biological function and mechanism. The SMART database (http://smart.embl-heidelberg.de/smart) is the primary target list for the project. The practical issues of obtaining soluble and crystallizable representatives for each sequence family will be discussed. The question of how much can be learned about signaling mechanisms from elucidating the structure of one representative protein per sequence family will be considered. Examples illustrating issues of principle and practice will be drawn from recent work on VHS and other domains. Acta Cryst. (2002 A Structural Genomics research program at CARB that seeks to infer the function of so-called hypothetical proteins from the structural information has yielded so far some 25 structures. The structures exhibit both previously known and novel folds. I will review the results provide specific examples and assess the power and limits of this approach. The genomes of Staphylococcus aureus and Streptococcus pyogenes, two important human pathogens, encode a variety of virulence factors, some of which have been clearly linked to disease. These include toxins such as staphylococcal enterotoxin A (SEA) and toxic shock syndrome toxin (TSST). These form a family of superantigens (SAgs) with a common fold and the ability to severely disrupt the human immune system by binding to both T-cell receptors and MHC class II molecules. Keywords: STRUCTURAL GENOMICS, SIGNAL TRANSDUCTION, PROTEIN TRANSPORT Keywords: STRUCTURAL GENOMICS HYPOTHETICAL PROTEINSThe Staphylococcus aureus genome also encodes a cluster of SAg-like genes whose functions are unknown. These genes are clustered on a putative pathogenicity island, implying a role in virulence. We crystallized one of these proteins, SET3, and solved and refined its structure at 1.9 Å resolution (R = 20.5%, Rfree = 24.0%). SET3 has the characteristic SAg-family fold, consistent with its sequence similarity (26% identity to TSST). Residues implicated in Tcell receptor and MHC binding in the SAgs are changed in SET3, however, and we have shown that SET3 does not have SAg activity. On the other hand, there are strong indications from seroconversion rates and antibody titres that SET3 has a role in pathogenicity. In the crystal, SET3 forms a dimer with a highly positively charged surface. Dimer formation occurs primarily through an extended β -hairpin that differentiates SET3 from other SAg-family proteins. We have shown that SET3 binds to DNA, which stabilizes SET3 dimer formation, but we hypothesize that the 'true' ligands for SET3 are likely to be negatively charged cell surface molecules. The high-throughput structure determination platform developed at Structural GenomiX is being utilized to increase the efficiency and effectiveness of the drug-discovery process. Parallelization increases the crystallization succes...