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(-) Description

Title :  THE CRYSTAL STRUCTURE OF KETO/OXOACID FERREDOXIN OXIDOREDUCTASE, GAMMA SUBUNIT FROM GEOBACTER SULFURREDUCENS PCA
 
Authors :  K. Tan, R. Zhang, C. Hatzos, K. Buck, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  27 Aug 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, R. Zhang, C. Hatzos, K. Buck, A. Joachimiak
The Crystal Structure Of Keto/Oxoacid Ferredoxin Oxidoreductase, Gamma Subunit From Geobacter Sulfurreducens Pca
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KETO/OXOACID FERREDOXIN OXIDOREDUCTASE, GAMMA SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GSU1470
    Organism Scientific: GEOBACTER SULFURREDUCENS
    Organism Taxid: 243231
    Strain: PCA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , GLN A:15 , GLY A:16 , LEU A:17 , ILE A:18 , HOH A:185 , ARG B:157BINDING SITE FOR RESIDUE SO4 A 183
2AC2SOFTWAREARG A:157 , GLY B:13 , GLN B:15 , GLY B:16 , LEU B:17 , ILE B:18 , HOH B:190BINDING SITE FOR RESIDUE SO4 B 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ON3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ON3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ON3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ON3)

(-) Exons   (0, 0)

(no "Exon" information available for 3ON3)

(-) 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    
   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:169
 aligned with Q74D49_GEOSL | Q74D49 from UniProtKB/TrEMBL  Length:182

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
         Q74D49_GEOSL     4 RYEIRFSGAGGQGLILAGVIMAEAASIYDGKQAVQSQSYGPEARGGASKSEVIISDGPVDYPKATQCDALLALTQEACDKYSADLKEGGVLLVDSDLVTKLPPGNYQTTAFNIINTAKNDVGREIVANIVALGAMVALTGVVSKEAAEKAVLSRVPEAFVELNRKAFQMGFEKALAA 180
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhh...eeeeeeee........eeeeeeee..--------...eeee.hhhhhhhh........eeeee............eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on3 A   4 RYEIRFSGAGGQGLILAGVImAEAASIYDGKQAVQSQSYGPEARGGASKSEVIISDG--------QCDALLALTQEACDKYSADLKEGGVLLVDSDLVTKLPPGNYQTTAFNIINTAKNDVGREIVANIVALGAmVALTGVVSKEAAEKAVLSRVPEAFVELNRKAFQmGFEKALAA 180
                                    13        23|       33        43        53      |  -     |  73        83        93       103       113       123       133    |  143       153       163       173       
                                               24-MSE                              60       69                                                                  138-MSE                           172-MSE    


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Q74D49_GEOSL | Q74D49 from UniProtKB/TrEMBL  Length:182

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
         Q74D49_GEOSL     2 SGRYEIRFSGAGGQGLILAGVIMAEAASIYDGKQAVQSQSYGPEARGGASKSEVIISDGPVDYPKATQCDALLALTQEACDKYSADLKEGGVLLVDSDLVTKLPPGNYQTTAFNIINTAKNDVGREIVANIVALGAMVALTGVVSKEAAEKAVLSRVPEAFVELNRKAFQMGFEKALAAKK 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------POR-3on3B01 B:13-175                                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) -----------POR-3on3B02 B:13-175                                                                                                                                               ------- Pfam domains (2)
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhh.....eeeeeeee..--....eeeeeeee.....----..eeeeee.hhhhhhhhh..eeeeeeeeee............eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on3 B   2 AGRYEIRFSGAGGQGLILAGVImAEAASIYDGKQAVQSQSYGP--RGGASKSEVIISDGPVD----TQCDALLALTQEACDKYSADLKEGGVLLVDSDLVTKLPPGNYQTTAFNIINTAKNDVGREIVANIVALGAmVALTGVVSKEAAEKAVLSRVPEAFVELNRKAFQmGFEKALAAKK 182
                                    11        21  |     31        41  |  |  51        61 |    | 71        81        91       101       111       121       131      |141       151       161       171|      181 
                                                 24-MSE              44 47              63   68                                                                   138-MSE                           172-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  (0, 0)

(no "SCOP Domain" information available for 3ON3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ON3)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: POR] (1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q74D49_GEOSL | Q74D49)
molecular function
    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.
    GO:0016730    oxidoreductase activity, acting on iron-sulfur proteins as donors    Catalysis of an oxidation-reduction (redox) reaction in which an iron-sulfur protein acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0016903    oxidoreductase activity, acting on the aldehyde or oxo group of donors    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0006113    fermentation    The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
    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.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

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