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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN VC1974 FROM VIBRIO CHOLERAE, PFAM ABHYDROLASE
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  01 Oct 03  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Hydrolase, Nysgxrc, New York Sgx Research Center For Structural Genomics, Psi, Protein Structure Initiative, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Gorman, L. Shapiro
Structural Genomics Target Nysgrc-T920 Related To A/B Hydrolase Fold.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN VC1974
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28A DERIVED CUSTOM VECTOR
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneVC1974
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1R3D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R3D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R3D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R3D)

(-) Exons   (0, 0)

(no "Exon" information available for 1R3D)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:257
 aligned with Q9KQM4_VIBCH | Q9KQM4 from UniProtKB/TrEMBL  Length:263

    Alignment length:264
                             1                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259    
         Q9KQM4_VIBCH     - -MLSNQLHFAKPTARTPLVVLVHGLLGSGADWQPVLSHLARTQCAALTLDLPGHGTNPERHCDNFAEAVEMIEQTVQAHVTSEVPVILVGYSLGGRLIMHGLAQGAFSRLNLRGAIIEGGHFGLQENEEKAARWQHDQQWAQRFSQQPIEHVLSDWYQQAVFSSLNHEQRQTLIAQRSANLGSSVAHMLLATSLAKQPYLLPALQALKLPIHYVCGEQDSKFQQLAESSGLSYSQVAQAGHNVHHEQPQAFAKIVQAMIHSIID 263
               SCOP domains d1r3da_ A: Hypothetical protein VC1974                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1r3dA00 A:0-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.........eeeee.....hhhhhhhhhhhhh....eeeee.........-------hhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee..hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r3d A   0 SLLSNQLHFAKPTARTPLVVLVHGLLGSGADWQPVLSHLARTQCAALTLDLPGHGTNP-------AEAVEmIEQTVQAHVTSEVPVILVGYSLGGRLImHGLAQGAFSRLNLRGAIIEGGHFGLQENEEKAARWQHDQQWAQRFSQQPIEHVLSDWYQQAVFSSLNHEQRQTLIAQRSANLGSSVAHmLLATSLAKQPYLLPALQALKLPIHYVCGEQDSKFQQLAESSGLSYSQVAQAGHNVHHEQPQAFAKIVQAmIHSIID 263
                                     9        19        29        39        49       | -     |  69|       79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259    
                                                                                    57      65    |                          98-MSE                                                                                  187-MSE                                                               257-MSE  
                                                                                                 70-MSE                                                                                                                                                                                             

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R3D)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9KQM4_VIBCH | Q9KQM4)
molecular function
    GO:0070205    2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity    Catalysis of the reaction: 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate = (1R,6R)-2-succinyl-6-hydroxycyclohexa-2,4-diene-1-carboxylate + pyruvate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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(-) Related Entries Specified in the PDB File

t920 RELATED ID: NYSGXRC-T920 RELATED DB: TARGETDB