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(-) Description

Title :  QUATERNARY COMPLEX STRUCTURE OF GLUCONATE 5-DEHYDROGENASE FROM STREPTOCOCCUS SUIS TYPE 2
 
Authors :  H. Peng, F. Gao, Q. Zhang, Y. Liu, G. F. Gao
Date :  18 Jul 10  (Deposition) - 15 Dec 10  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Zhang, H. Peng, F. Gao, Y. Liu, H. Cheng, J. Thompson, G. F. Gao
Structural Insight Into The Catalytic Mechanism Of Gluconat 5-Dehydrogenase From Streptococcus Suis: Crystal Structures Of The Substrate-Free And Quaternary Complex Enzymes.
Protein Sci. V. 18 294 2009
PubMed-ID: 19177572  |  Reference-DOI: 10.1002/PRO.32

(-) Compounds

Molecule 1 - DEHYDROGENASE WITH DIFFERENT SPECIFICITIES
    ChainsA
    EC Number1.1.1.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneIDNO, SSU05_1225
    Organism ScientificSTREPTOCOCCUS SUIS
    Organism Taxid391295
    Strain05ZYH33

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GCO1Ligand/IonGLUCONIC ACID
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GCO4Ligand/IonGLUCONIC ACID
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GCO2Ligand/IonGLUCONIC ACID
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:150 , MET A:151 , PRO A:193 , GLY A:194 , NAP A:273 , GCO A:274 , HOH A:479BINDING SITE FOR RESIDUE CA A 272
2AC2SOFTWAREGLY A:21 , SER A:23 , TYR A:24 , GLY A:25 , ILE A:26 , ASP A:45 , ILE A:46 , LEU A:50 , CYS A:70 , ASP A:71 , VAL A:72 , ASN A:98 , ALA A:99 , GLY A:100 , ILE A:148 , CYS A:149 , TYR A:163 , LYS A:167 , THR A:198 , CA A:272 , GCO A:274 , HOH A:293 , HOH A:315 , HOH A:317 , HOH A:323 , HOH A:348 , HOH A:477BINDING SITE FOR RESIDUE NAP A 273
3AC3SOFTWAREILE A:102 , ARG A:104 , SER A:150 , MET A:152 , ARG A:157 , VAL A:160 , TYR A:163 , CA A:272 , NAP A:273 , HOH A:478 , HOH A:479 , HOH A:482BINDING SITE FOR RESIDUE GCO A 274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O03)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O03)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O03)

(-) Exons   (0, 0)

(no "Exon" information available for 3O03)

(-) Sequences/Alignments

Asymmetric 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    
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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:254
 aligned with A4VVQ2_STRSY | A4VVQ2 from UniProtKB/TrEMBL  Length:271

    Alignment length:266
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      
         A4VVQ2_STRSY     4 QFSLDQFSLKGKIALVTGASYGIGFAIASAYAKAGATIVFNDINQELVDRGMAAYKAAGINAHGYVCDVTDEDGIQAMVAQIESEVGIIDILVNNAGIIRRVPMIEMTAAQFRQVIDIDLNAPFIVSKAVIPSMIKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTKNIASEYGEANIQCNGIGPGYIATPQTAPLRELQKDGSRHPFDQFIIAKTPAARWGEAEDLMGPAVFLASDASNFVNGHILYVDGGILAYIGKQP 269
               SCOP domains d3o03a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------adh_short-3o03A01 A:15-182                                                                                                                                              --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee........------------hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o03 A   4 QFSLDQFSLKGKIALVTGASYGIGFAIASAYAKAGATIVFNDINQELVDRGMAAYKAAGINAHGYVCDVTDEDGIQAMVAQIESEVGIIDILVNNAGIIRRVPMIEMTAAQFRQVIDIDLNAPFIVSKAVIPSMIKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTKNIASEYGEANIQCNGIGPGYIATPQT------------HPFDQFIIAKTPAARWGEAEDLMGPAVFLASDASNFVNGHILYVDGGILAYIGKQP 269
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       | -         -|      223       233       243       253       263      
                                                                                                                                                                                                                               201          214                                                       

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  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 Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 3CXT: 1,1)

(no "CATH Domain" information available for 3O03, only for superseded entry 3CXT replaced by 3O03)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (A4VVQ2_STRSY | A4VVQ2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A4VVQ2_STRSY | A4VVQ23cxr

(-) Related Entries Specified in the PDB File

3cxr