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(-) Description

Title :  CRYSTAL STRUCTURE OF VC2308 PROTEIN
 
Authors :  E. Niedzialkowska, Z. Wawrzak, M. Chruszcz, P. Porebski, T. Skarina, X S. Grimshaw, M. Cymborowski, A. Savchenko, W. F. Anderson, W. Minor, C Structural Genomics Of Infectious Diseases (Csgid)
Date :  10 Sep 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Csgid, Structural Genomics, Vibrio Cholerae, Center For Structural Genomics Of Infectious Diseases, Dj-1 Superfamily, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Niedzialkowska, Z. Wawrzak, M. Chruszcz, P. Porebski, T. Skarina, X. Huang, S. Grimshaw, M. Cymborowski, A. Savchenko, W. F. Anderson, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Vc2308 Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-METHYL-5(B-HYDROXYETHYL)-THIAZOLE MONOPHOSPHATE BIOSYNTHESIS ENZYME
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMCSG7
    Expression System StrainBL21 DE3 GOLD MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneVC2308, VC_2308
    Organism ScientificVIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid243277
    Other DetailsCYS AT RESIDUE 108
    StrainN16961
 
Molecule 2 - 4-METHYL-5(B-HYDROXYETHYL)-THIAZOLE MONOPHOSPHATE BIOSYNTHESIS ENZYME
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMCSG7
    Expression System StrainBL21 DE3 GOLD MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneVC2308, VC_2308
    Organism ScientificVIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid243277
    Other DetailsCSX AT RESIDUE 108
    StrainN16961

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CSX1Mod. Amino AcidS-OXY CYSTEINE
3MSE11Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:51 , GLY B:77 , VAL B:78BINDING SITE FOR RESIDUE CL B 206
2AC2SOFTWAREALA B:40 , GLY B:42 , THR B:60 , LEU B:61 , GLU B:62 , HOH B:335BINDING SITE FOR RESIDUE NA B 207
3AC3SOFTWAREHIS A:129 , HOH A:330 , ARG B:31 , PRO B:186 , HOH B:301BINDING SITE FOR RESIDUE CL B 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OT1)

(-) Exons   (0, 0)

(no "Exon" information available for 3OT1)

(-) 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:199
 aligned with Q9KPQ8_VIBCH | Q9KPQ8 from UniProtKB/TrEMBL  Length:205

    Alignment length:199
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195         
         Q9KPQ8_VIBCH     6 SKRILVPVAHGSEEMETVIIVDTLVRAGFQVTMAAVGDKLQVQGSRGVWLTAEQTLEACSAEAFDALALPGGVGGAQAFADSTALLALIDAFSQQGKLVAAICATPALVFAKQQKFVGARMTCHPNFFDHIPSERLSRQRVCYYATQHLLTSQGPGTALEFALAMIALLAGVELAQHVAAPMVLHPQQLTELSGFIDAQ 204
               SCOP domains d3ot1a_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhh..eeeeee.....eee.....eee..ee.hhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh..............hhhhhhhh.........eeeehhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ot1 A   6 SKRILVPVAHGSEEmETVIIVDTLVRAGFQVTmAAVGDKLQVQGSRGVWLTAEQTLEACSAEAFDALALPGGVGGAQAFADSTALLALIDAFSQQGKLVAAICATPALVFAKQQKFVGARmTCHPNFFDHIPSERLSRQRVCYYATQHLLTSQGPGTALEFALAmIALLAGVELAQHVAAPmVLHPQQLTELSGFIDAQ 204
                                    15    |   25        35  |     45        55        65        75        85        95       105       115       125|      135       145       155       165    |  175       185 |     195         
                                         20-MSE            38-MSE                                                                                 126-MSE                                     170-MSE          187-MSE             

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q9KPQ8_VIBCH | Q9KPQ8 from UniProtKB/TrEMBL  Length:205

    Alignment length:196
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194      
         Q9KPQ8_VIBCH     5 MSKRILVPVAHGSEEMETVIIVDTLVRAGFQVTMAAVGDKLQVQGSRGVWLTAEQTLEACSAEAFDALALPGGVGGAQAFADSTALLALIDAFSQQGKLVAAICATPALVFAKQQKFVGARMTCHPNFFDHIPSERLSRQRVCYYATQHLLTSQGPGTALEFALAMIALLAGVELAQHVAAPMVLHPQQLTELSGF 200
               SCOP domains d3ot1b_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------DJ-1_PfpI-3ot1B01 B:35-175                                                                                                                   ------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------DJ-1_PfpI-3ot1B02 B:35-175                                                                                                                   ------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh..eeeeee.....eee.....eee..ee.hhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh..............hhhhhhhh.........eeeehhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ot1 B   5 mSKRILVPVAHGSEEmETVIIVDTLVRAGFQVTmAAVGDKLQVQGSRGVWLTAEQTLEACSAEAFDALALPGGVGGAQAFADSTALLALIDAFSQQGKLVAAIcATPALVFAKQQKFVGARmTCHPNFFDHIPSERLSRQRVCYYATQHLLTSQGPGTALEFALAmIALLAGVELAQHVAAPmVLHPQQLTELSGF 200
                            |       14     |  24        34   |    44        54        64        74        84        94       104   |   114       124 |     134       144       154       164     | 174       184  |    194      
                            5-MSE         20-MSE            38-MSE                                                               108-CSX           126-MSE                                     170-MSE          187-MSE         

   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OT1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KPQ8_VIBCH | Q9KPQ8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0019172    glyoxalase III activity    Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0019249    lactate biosynthetic process    The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid.
    GO:0019243    methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione    The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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