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(-) Description

Title :  CRYSTAL STRUCTURE OF UNKNOWN FUNCTION PROTEIN VCA1059
 
Authors :  C. Chang, A. Sather, S. Moy, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  10 Aug 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vibrio Cholerae, Unknown Function, Structural Genomics, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, A. Sather, S. Moy, L. Freeman, A. Joachimiak
Crystal Structure Of Unknown Function Protein Vca1059.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0217 PROTEIN VC_A1059
    Atcc: 39315
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VC_A1059
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
    Organism Taxid: 243277
    Strain: EL TOR INABA N16961

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2MSE17Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:138 , SER A:179 , LEU A:180 , LYS A:183BINDING SITE FOR RESIDUE ACY A 301
2AC2SOFTWAREMSE B:136 , LEU B:180 , LYS B:183 , LEU B:185BINDING SITE FOR RESIDUE ACY B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QWV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QWV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QWV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QWV)

(-) Exons   (0, 0)

(no "Exon" information available for 2QWV)

(-) 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:188
 aligned with TRMYL_VIBCH | Q9KKP3 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:202
                             1                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  
          TRMYL_VIBCH     - -MRSFILRARSAPTDSQRLLDEIGGKCHTEILAHCMMNSLFTAQSHREDVVIHLVLESTRDYSRTITVEANEISDVGGFHEAALIALLVKALDASVGMGKEQTRVVQPGLTVRTISFEALLGELAEHHSLYMMDKKGDSIRDIKIGPNPCFILTDHIPMPKKSGNSMKRLGVEKISLGPKMLFASQCVTLIHNEIDHQEAGW 201
               SCOP domains -d2qwva1 A:5-205 Uncharacterized protein VCA1059                                                                                                                                                           SCOP domains
               CATH domains 2qwvA00 A:4-205  [code=3.40.1280.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.hhhhhhhh......hhhhhhhhhhhhh........eeeeeeeee.....eeeeee....----..hhhhhhhhhhhhhhhh.......eeeee..eeee..hhhhhhhhhhh..eeeee....ee.........eeeee..----------.......eeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwv A   4 TmRSFILRARSAPTDSQRLLDEIGGKCHTEILAHCmmNSLFTAQSHREDVVIHLVLESTRDYSRTITVEANEI----GFHEAALIALLVKALDASVGmGKEQTRVVQPGLTVRTISFEALLGELAEHHSLYmmDKKGDSIRDIKIGPNPCFILTD----------SmKRLGVEKISLGPKmLFASQCVTLIHNEIDHQEAGW 205
                             |      13        23        33     || 43        53        63        73  |    |83        93       103       113       123       133 ||    143       153    |    -     ||173       183|      193       203  
                             |                                39-MSE                               76   81                 101-MSE                           135-MSE                158        169|           184-MSE                 
                             5-MSE                             40-MSE                                                                                         136-MSE                           170-MSE                               


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with TRMYL_VIBCH | Q9KKP3 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:208
                                   1                                                                                                                                                                                                        
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193        
          TRMYL_VIBCH     - -------MRSFILRARSAPTDSQRLLDEIGGKCHTEILAHCMMNSLFTAQSHREDVVIHLVLESTRDYSRTITVEANEISDVGGFHEAALIALLVKALDASVGMGKEQTRVVQPGLTVRTISFEALLGELAEHHSLYMMDKKGDSIRDIKIGPNPCFILTDHIPMPKKSGNSMKRLGVEKISLGPKMLFASQCVTLIHNEIDHQEAGW 201
               SCOP domains d2qwvb_ B: Uncharacterized protein VCA1059                                                                                                                                                                       SCOP domains
               CATH domains 2qwvB00 B:-2-205  [code=3.40.1280.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee.hhhhhhhh......hhhhhhhhhhhhh........eeeeeeeee.....eeeeee.....---..hhhhhhhhhhhhhhh........eeeee..eeee..hhhhhhhhhh...eeeee....ee.hhh.....eeeeee..--------hhhhhh..eeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwv B  -2 SNAmRNTmRSFILRARSAPTDSQRLLDEIGGKCHTEILAHCmmNSLFTAQSHREDVVIHLVLESTRDYSRTITVEANEIS---GFHEAALIALLVKALDASVGmGKEQTRVVQPGLTVRTISFEALLGELAEHHSLYmmDKKGDSIRDIKIGPNPCFILTDH--------NSmKRLGVEKISLGPKmLFASQCVTLIHNEIDHQEAGW 205
                               |   | 7        17        27        37 ||     47        57        67        77   |    87        97   |   107       117       127       137       147       157 |       -| |    177      |187       197        
                               1-MSE                                39-MSE                                77  81                 101-MSE                           135-MSE                 159      168 |           184-MSE                 
                                   5-MSE                             40-MSE                                                                                         136-MSE                           170-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QWV)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRMYL_VIBCH | Q9KKP3)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.
    GO:0008175    tRNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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