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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE NADH DEHYDROGENASE/NAD(P)H NITROREDUCTASE (BDI_1728) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.86 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Mar 10  (Deposition) - 05 May 10  (Release) - 05 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Nadh Dehydrogenase/Nad(P)H Nitroreductase (Bdi_1728) From Parabacteroides Distasonis Atcc 8503 At 1. 86 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE NADH DEHYDROGENASE/NAD(P)H NITROREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 24-194
    Gene: BDI_1728
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE12Mod. Amino AcidSELENOMETHIONINE
4UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , LYS A:38 , SER A:39 , ARG A:41 , PHE A:92 , VAL A:139 , TRP A:140 , THR A:141 , ALA A:142 , ARG A:149 , LYS A:181 , LYS A:183 , HOH A:312 , HOH A:319 , HOH A:327 , PRO B:64 , SER B:65 , SER B:66 , ASP B:68 , ASP B:119BINDING SITE FOR RESIDUE FMN A 301
2AC2SOFTWAREPRO A:64 , SER A:65 , SER A:66 , ASP A:68 , ASP A:119 , ARG B:37 , LYS B:38 , SER B:39 , ARG B:41 , PHE B:92 , MSE B:95 , VAL B:139 , TRP B:140 , THR B:141 , ALA B:142 , LYS B:181 , LYS B:183 , HOH B:309 , HOH B:333 , HOH B:386 , HOH B:406 , HOH B:494BINDING SITE FOR RESIDUE FMN B 301
3AC3SOFTWARELYS B:50BINDING SITE FOR RESIDUE CL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M5K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:144 -Pro A:145
2Tyr B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M5K)

(-) Exons   (0, 0)

(no "Exon" information available for 3M5K)

(-) 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:168
 aligned with A6LCR1_PARD8 | A6LCR1 from UniProtKB/TrEMBL  Length:194

    Alignment length:168
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186        
         A6LCR1_PARD8    27 ENQTLETILNRKSVRKYKDRPVEKEKIDKLIRAGMAAPSSRDRRPWEFIIVTDRKALDTMAEGLPFARMLKETRQAIVVCGDTIKSSNAWFLDCSAASQNLLLAAESMGLGAVWTAVYPYPDRIEIVRKELRLPDHIMPLNVIPVGYPMQKETPKNKYNVQQIHHNGW 194
               SCOP domains d3m5ka_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhh..ee..ee...hhhhhhhhhhhhh....eeeeeeeeee............hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m5k A  27 ENQTLETILNRKSVRKYKDRPVEKEKIDKLIRAGmAAPSSRDRRPWEFIIVTDRKALDTmAEGLPFARmLKETRQAIVVCGDTIKSSNAWFLDCSAASQNLLLAAESmGLGAVWTAVYPYPDRIEIVRKELRLPDHImPLNVIPVGYPmQKETPKNKYNVQQIHHNGW 194
                                    36        46        56    |   66        76        86        96       106       116       126       136       146       156       166       176       186        
                                                             61-MSE                   86-MSE   95-MSE                                134-MSE                       164-MSE    175-MSE               


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with A6LCR1_PARD8 | A6LCR1 from UniProtKB/TrEMBL  Length:194

    Alignment length:168
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186        
         A6LCR1_PARD8    27 ENQTLETILNRKSVRKYKDRPVEKEKIDKLIRAGMAAPSSRDRRPWEFIIVTDRKALDTMAEGLPFARMLKETRQAIVVCGDTIKSSNAWFLDCSAASQNLLLAAESMGLGAVWTAVYPYPDRIEIVRKELRLPDHIMPLNVIPVGYPMQKETPKNKYNVQQIHHNGW 194
               SCOP domains d3m5kb_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------Nitroreductase-3m5kB01 B:34-173                                                                                                             --------------------- Pfam domains (1)
           Pfam domains (2) -------Nitroreductase-3m5kB02 B:34-173                                                                                                             --------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhh..ee..ee...hhhhhhhhhhhhh....eeeeeeeeee............hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m5k B  27 ENQTLETILNRKSVRKYKDRPVEKEKIDKLIRAGmAAPSSRDRRPWEFIIVTDRKALDTmAEGLPFARmLKETRQAIVVCGDTIKSSNAWFLDCSAASQNLLLAAESmGLGAVWTAVYPYPDRIEIVRKELRLPDHImPLNVIPVGYPmQKETPKNKYNVQQIHHNGW 194
                                    36        46        56    |   66        76        86        96       106       116       126       136       146       156       166       176       186        
                                                             61-MSE                   86-MSE   95-MSE                                134-MSE                       164-MSE    175-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M5K)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Nitroreductase] (9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6LCR1_PARD8 | A6LCR1)
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.
    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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