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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE COMPLEXED WITH NADP(H)
 
Authors :  Y. Kim, H. J. Park, S. N. Kwak, J. S. Lee, T. K. Oh, M. H. Kim
Date :  31 Mar 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Reductase, Sdr Family, Oxidoreductase, Triphenylmethane Reduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Kim, Y. Kim, H. J. Park, J. S. Lee, S. N. Kwak, W. H. Jung, S. G. Lee, D. Kim, Y. C. Lee, T. K. Oh
Structural Insight Into Bioremediation Of Triphenylmethane Dyes By Citrobacter Sp. Triphenylmethane Reductase.
J. Biol. Chem. V. 283 31981 2008
PubMed-ID: 18782772  |  Reference-DOI: 10.1074/JBC.M804092200

(-) Compounds

Molecule 1 - TRIPHENYLMETHANE REDUCTASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETA GAMI (DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: CITROBACTER SP. MY-5
    Organism Taxid: 308866
 
Molecule 2 - TRIPHENYLMETHANE REDUCTASE
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETA GAMI (DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: CITROBACTER SP. MY-5
    Organism Taxid: 308866

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2VRC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VRC)

(-) 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:285
 aligned with Q2TNI4_9ENTR | Q2TNI4 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     
         Q2TNI4_9ENTR     1 MSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhh.eeee....hhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh..hhhhhhhhhhhhhhh....eeeeee...hhhh...hhhhhhhhheeee.....ee...hhhhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrc A   1 FSIAVTGATGQLGGLVIQHLmAAVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFmVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |  240       250       260       270       280     
                                               21-MSE                                                                                                                                                                                                               235-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with Q2TNI4_9ENTR | Q2TNI4 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     
         Q2TNI4_9ENTR     1 MSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhh..eeee....hhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhhhhhhhhhh...eeeeee...hhhh.hhhhhhhhhhheeee.....ee...hhhhhhhhhhhhhhh.....eeeee.....eehhhhhhhhhhhhh...eeee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrc B   1 FSIAVTGATGQLGGLVIQHLmAAVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFmVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |  240       250       260       270       280     
                                               21-MSE                                                                                                                                                                                                               235-MSE                                              


Chain C from PDB  Type:PROTEIN  Length:285
 aligned with Q2TNI4_9ENTR | Q2TNI4 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     
         Q2TNI4_9ENTR     1 MSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhh..hhh.eeeee.....hhhhhhh..eeee....hhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh..hhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh..eeee.....ee...hhhhhhhhhhhhh.......eeeee.....eehhhhhhhhhhhh....eeee...hhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrc C   1 FSIAVTGATGQLGGLVIQHLmAAVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFmVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |  240       250       260       270       280     
                                               21-MSE                                                                                                                                                                                                               235-MSE                                              


Chain D from PDB  Type:PROTEIN  Length:285
 aligned with Q2TNI4_9ENTR | Q2TNI4 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     
         Q2TNI4_9ENTR     1 MSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NmrA-2vrcD01 D:3-227                                                                                                                                                                                                             ---------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --NmrA-2vrcD02 D:3-227                                                                                                                                                                                                             ---------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --NmrA-2vrcD03 D:3-227                                                                                                                                                                                                             ---------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --NmrA-2vrcD04 D:3-227                                                                                                                                                                                                             ---------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhh..eeee....hhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhheeee..........hhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrc D   1 FSIAVTGATGQLGGLVIQHLmAAVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYATRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFmVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |  240       250       260       270       280     
                                               21-MSE                                                                                                                                                                                                               235-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  (0, 0)

(no "SCOP Domain" information available for 2VRC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VRC)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Family: NmrA (22)
(-)
Citrobacter sp. MY-5 (3)
1aNmrA-2vrcD01D:3-227
1bNmrA-2vrcD02D:3-227
1cNmrA-2vrcD03D:3-227
1dNmrA-2vrcD04D:3-227

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q2TNI4_9ENTR | Q2TNI4)
molecular function
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2TNI4_9ENTR | Q2TNI4: 2jl1 2vrb

(-) Related Entries Specified in the PDB File

2vrb CRYSTAL STRUCTURE OF THE CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE COMPLEXED WITH NADP(H)