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(-) Description

Title :  STRUCTURAL INSIGHT INTO BIOREMEDIATION OF TRIPHENYLMETHANE DYES BY CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE
 
Authors :  Y. Kim, H. J. Park, S. N. Kwak, M. H. Kim
Date :  02 Sep 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Triphenylmethane Reductase, Oxidoreductase, Bioremediation, Triphenylmethane (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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETA GAMI (DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 2-287
    Organism Scientific: CITROBACTER SP. MY-5
    Organism Taxid: 308866

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , THR A:9 , GLY A:10 , GLN A:11 , LEU A:12 , ARG A:34 , LYS A:38 , GLY A:52 , ASP A:53 , TYR A:54 , ASN A:55 , ILE A:73 , SER A:74 , GLY A:75 , PRO A:76 , HIS A:77 , ALA A:141 , LEU A:142 , TYR A:143 , ARG A:175 , HOH A:2003 , HOH A:2006 , HOH A:2007 , HOH A:2011 , HOH A:2031 , HOH A:2162 , HOH A:2164BINDING SITE FOR RESIDUE NAP A1288
2AC2SOFTWARETHR A:144 , SER A:172 , VAL A:173 , GLU A:177 , SER A:200 , GLN A:202 , THR A:275 , HOH A:2118 , HOH A:2159 , HOH A:2165BINDING SITE FOR RESIDUE GOL A1289
3AC3SOFTWAREGLU A:111 , LEU A:122 , GLU A:125 , TYR A:126 , ARG A:129BINDING SITE FOR RESIDUE GOL A1290
4AC4SOFTWARELYS A:69 , HIS A:101 , THR A:136 , VAL A:185 , GLU A:188 , GLY A:190 , HIS A:191 , GLU A:192BINDING SITE FOR RESIDUE GOL A1291
5AC5SOFTWARETYR A:107 , ALA A:108 , PHE A:109 , ALA A:141 , LEU A:142 , ASN A:171 , GLU A:259 , ALA A:260 , HOH A:2142 , HOH A:2167BINDING SITE FOR RESIDUE GOL A1292
6AC6SOFTWARETYR A:78 , ASP A:79 , ASN A:80 , THR A:81 , ARG A:95 , THR A:130 , THR A:131BINDING SITE FOR RESIDUE GOL A1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JL1)

(-) Exons   (0, 0)

(no "Exon" information available for 2JL1)

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

    Alignment length:287
                                    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 MSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQALKM 287
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --NmrA-2jl1A01 A:3-227                                                                                                                                                                                                             ------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhh...hhh.eeeee.....hhhhhhh..eeee....hhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh..hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhheeee..........hhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jl1 A   1 FSIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFTEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQALKM 287
                                    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
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2JL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JL1)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  2jl1
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 Related Entries

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

UniProtKB/TrEMBL
        Q2TNI4_9ENTR | Q2TNI4: 2vrb 2vrc

(-) Related Entries Specified in the PDB File

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