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(-) Description

Title :  CRYSTAL STRUCTURE OF A GFO/IDH/MOCA FAMILY OXIDOREDUCTASE FROM VIBRIO CHOLERAE
 
Authors :  K. R Rajashankar, J. A. Reynes, R. Kniewel, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  09 Sep 04  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics; Protein Structure Initiative; Nysgxrc; T1536; Vca1048; Gfo/Idh/Moca Family Oxidoreductase, Psi, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R Rajashankar, J. A. Reynes, R. Kniewel, C. D. Lima
Crystal Structure Of A Gfo/Idh/Moca Family Oxidoreductase From Vibrio Cholerae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, GFO/IDH/MOCA FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Strain: B834, DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VCA1048
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: GFO/IDH/MOCA FAMILY OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 29)

Asymmetric/Biological Unit (2, 29)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:134 , HOH A:1032 , HOH A:1046 , HOH A:1066BINDING SITE FOR RESIDUE NI A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:94 -Pro A:95
2Lys B:94 -Pro B:95
3Lys C:94 -Pro C:95
4Lys D:94 -Pro D:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XEA)

(-) 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:311
 aligned with Q9KKQ4_VIBCH | Q9KKQ4 from UniProtKB/TrEMBL  Length:311

    Alignment length:311
                             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       269       279       289       299       309 
         Q9KKQ4_VIBCH     - -MKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFGITTEHVTASYDNVAYLFDSFTQGKMWRDNQESRVALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 310
               SCOP domains d1xeaa1 A:2-122,A:267-312 Putative oxidoreductase VCA1048                                                                d1xeaa2 A:123-266 Putative oxidoreductase VCA1048                                                                                               d1xeaa1 A:2-122,A:267-312                      SCOP domains
               CATH domains 1xeaA01 A:2-120 NAD(P)-binding Rossmann-like Domain                                                                    1xeaA02 A:121-312 Dihydrodipicolinate Reductase; domain 2                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.........hhhhhhh..eeee..hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh......eeeeeee......hhhhhhhh.hhhhhhhhh.........eeeeeeee..eeeeeeeeeee..eeeeeeee......eeeeeeee..eeeee....eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xea A   2 SLKIAmIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVmIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHmSEGLLARLDVQWQTGDTLLHASmNRQFGITTEHVTASYDNVAYLFDSFTQGKmWRDNQESRVALKDWTPmLASKGFDAmVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 312
                                 |  11        21        31        41        51        61      | 71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211   |   221       231       241   |   251       261|      271       281       291       301       311 
                                 7-MSE                                                       68-MSE                                                                                                                     192-MSE                215-MSE                       245-MSE          262-MSE  271-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Q9KKQ4_VIBCH | Q9KKQ4 from UniProtKB/TrEMBL  Length:311

    Alignment length:311
                             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       269       279       289       299       309 
         Q9KKQ4_VIBCH     - -MKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFGITTEHVTASYDNVAYLFDSFTQGKMWRDNQESRVALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 310
               SCOP domains d1xeab1 B:2-122,B:267-312 Putative oxidoreductase VCA1048                                                                d1xeab2 B:123-266 Putative oxidoreductase VCA1048                                                                                               d1xeab1 B:2-122,B:267-312                      SCOP domains
               CATH domains 1xeaB01 B:2-120 NAD(P)-binding Rossmann-like Domain                                                                    1xeaB02 B:121-312 Dihydrodipicolinate Reductase; domain 2                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh...........hhhhh..eeee..hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh......eeeeeee......hhhhhhhhhhhhhhhhh..........eeeeeeee..eeeeeeeeeee..eeeeeeee......eeeeeeee..eeeee....eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xea B   2 SLKIAmIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVmIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHmSEGLLARLDVQWQTGDTLLHASmNRQFGITTEHVTASYDNVAYLFDSFTQGKmWRDNQESRVALKDWTPmLASKGFDAmVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 312
                                 |  11        21        31        41        51        61      | 71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211   |   221       231       241   |   251       261|      271       281       291       301       311 
                                 7-MSE                                                       68-MSE                                                                                                                     192-MSE                215-MSE                       245-MSE          262-MSE  271-MSE                                     


Chain C from PDB  Type:PROTEIN  Length:311
 aligned with Q9KKQ4_VIBCH | Q9KKQ4 from UniProtKB/TrEMBL  Length:311

    Alignment length:311
                             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       269       279       289       299       309 
         Q9KKQ4_VIBCH     - -MKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFGITTEHVTASYDNVAYLFDSFTQGKMWRDNQESRVALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 310
               SCOP domains d1xeac1 C:2-122,C:267-312 Putative oxidoreductase VCA1048                                                                d1xeac2 C:123-266 Putative oxidoreductase VCA1048                                                                                               d1xeac1 C:2-122,C:267-312                      SCOP domains
               CATH domains 1xeaC01 C:2-120 NAD(P)-binding Rossmann-like Domain                                                                    1xeaC02 C:121-312 Dihydrodipicolinate Reductase; domain 2                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh....ee...hhhhhhh..eeee..hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh......eeeeeee......hhhhhhhhhhhhhhhhhh.........eeeeeeee..eeeeeeeeeee..eeeeeeee......eeeeeeee..eeeee....eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xea C   2 SLKIAmIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVmIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHmSEGLLARLDVQWQTGDTLLHASmNRQFGITTEHVTASYDNVAYLFDSFTQGKmWRDNQESRVALKDWTPmLASKGFDAmVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 312
                                 |  11        21        31        41        51        61      | 71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211   |   221       231       241   |   251       261|      271       281       291       301       311 
                                 7-MSE                                                       68-MSE                                                                                                                     192-MSE                215-MSE                       245-MSE          262-MSE  271-MSE                                     


Chain D from PDB  Type:PROTEIN  Length:311
 aligned with Q9KKQ4_VIBCH | Q9KKQ4 from UniProtKB/TrEMBL  Length:311

    Alignment length:311
                             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       269       279       289       299       309 
         Q9KKQ4_VIBCH     - -MKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFGITTEHVTASYDNVAYLFDSFTQGKMWRDNQESRVALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 310
               SCOP domains d1xead1 D:2-122,D:267-312 Putative oxidoreductase VCA1048                                                                d1xead2 D:123-266 Putative oxidoreductase VCA1048                                                                                               d1xead1 D:2-122,D:267-312                      SCOP domains
               CATH domains 1xeaD01 D:2-120 NAD(P)-binding Rossmann-like Domain                                                                    1xeaD02 D:121-312 Dihydrodipicolinate Reductase; domain 2                                                                                                                                        CATH domains
           Pfam domains (1) --GFO_IDH_MocA-1xeaD01 D:4-121                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --GFO_IDH_MocA-1xeaD02 D:4-121                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --GFO_IDH_MocA-1xeaD03 D:4-121                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --GFO_IDH_MocA-1xeaD04 D:4-121                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh....ee.hhhhhhhhh..eeee..hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh......eeeeeee......hhhhhhhhhhhhhhhhhh.........eeeeeeee..eeeeeeeeeee..eeeeeeee......eeeeeee...eeeee....eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xea D   2 SLKIAmIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVmIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCNLDDLHLTYHmSEGLLARLDVQWQTGDTLLHASmNRQFGITTEHVTASYDNVAYLFDSFTQGKmWRDNQESRVALKDWTPmLASKGFDAmVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 312
                                 |  11        21        31        41        51        61      | 71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211   |   221       231       241   |   251       261|      271       281       291       301       311 
                                 7-MSE                                                       68-MSE                                                                                                                     192-MSE                215-MSE                       245-MSE          262-MSE  271-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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9KKQ4_VIBCH | Q9KKQ4)
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.
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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