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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN (DDE_0787) FROM DESULFOVIBRIO DESULFURICANS SUBSP. AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Aug 08  (Deposition) - 19 Aug 08  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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 Nitroreductase In Complex Wit Fmn (Yp_387283. 1) From Desulfovibrio Desulfuricans G20 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE 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
    Gene: YP_387283.1, DDE_0787
    Organism Scientific: DESULFOVIBRIO DESULFURICANS SUBSP. DESULFURICANS STR. G20
    Organism Taxid: 207559

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE4Mod. Amino AcidSELENOMETHIONINE
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:123 , GLY B:43 , TYR B:91 , LYS B:95 , HOH B:263 , HOH B:314BINDING SITE FOR RESIDUE ACT B 178
2AC2SOFTWARETYR A:91 , LYS A:95 , GLY B:122 , GLU B:123 , HOH B:391BINDING SITE FOR RESIDUE ACT A 178
3AC3SOFTWAREGLY A:43 , LEU A:44 , HOH A:281 , HOH A:317BINDING SITE FOR RESIDUE ACT A 179
4AC4SOFTWAREARG A:14 , ARG A:15 , SER A:16 , ARG A:18 , TYR A:70 , ILE A:73 , TRP A:120 , LEU A:121 , GLY A:122 , GLU A:123 , SER A:159 , ARG A:161 , HOH A:212 , HOH A:226 , HOH A:248 , HOH A:252 , PRO B:41 , SER B:42 , GLY B:43 , ASN B:45 , LYS B:95 , HOH B:298BINDING SITE FOR RESIDUE FMN A 200
5AC5SOFTWAREPRO A:41 , SER A:42 , GLY A:43 , ASN A:45 , TYR A:91 , LYS A:95 , ARG B:14 , ARG B:15 , SER B:16 , ARG B:18 , TYR B:70 , TRP B:120 , LEU B:121 , GLY B:122 , GLU B:123 , SER B:159 , ARG B:161 , HOH B:207 , HOH B:227 , HOH B:272 , HOH B:367BINDING SITE FOR RESIDUE FMN B 200
6AC6SOFTWAREARG A:87 , PRO A:139 , PRO A:174 , GLN A:175 , SER B:158 , HOH B:227 , HOH B:280BINDING SITE FOR RESIDUE PGE B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E39)

(-) Exons   (0, 0)

(no "Exon" information available for 3E39)

(-) 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:175
 aligned with Q314Q8_DESAG | Q314Q8 from UniProtKB/TrEMBL  Length:177

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         Q314Q8_DESAG     3 TENPVLQAIRQRRSIRRYTDEAVSDEAVRLILEAGIWAPSGLNNQPCRFLVIRADDPRCDILAAHTRYGHIVRGAKVIILVFLDREAMYNEVKDHQAAGAAVQNMLLAAHALQLGAVWLGEIINQAATLLPALALDPARLSFEAAIAAGHPAQNGSSSRRPLAELLLEEPFPQPE 177
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeeee...hhhhhhhh...hhhhhhhh.eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh......eeeeeeeeee...........hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e39 A   3 TENPVLQAIRQRRSIRRYTDEAVSDEAVRLILEAGIWAPSGLNNQPCRFLVIRADDPRCDILAAHTRYGHIVRGAKVIILVFLDREAmYNEVKDHQAAGAAVQNmLLAAHALQLGAVWLGEIINQAATLLPALALDPARLSFEAAIAAGHPAQNGSSSRRPLAELLLEEPFPQPE 177
                                    12        22        32        42        52        62        72        82       |92       102    |  112       122       132       142       152       162       172     
                                                                                                                  90-MSE          107-MSE                                                                  


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q314Q8_DESAG | Q314Q8 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q314Q8_DESAG     3 TENPVLQAIRQRRSIRRYTDEAVSDEAVRLILEAGIWAPSGLNNQPCRFLVIRADDPRCDILAAHTRYGHIVRGAKVIILVFLDREAMYNEVKDHQAAGAAVQNMLLAAHALQLGAVWLGEIINQAATLLPALALDPARLSFEAAIAAGHPAQNGSSSRRPLAELLLEEPFP 174
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...........hhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhh..hhhhhhhh.eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh......eeeeeeeeee...........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e39 B   3 TENPVLQAIRQRRSIRRYTDEAVSDEAVRLILEAGIWAPSGLNNQPCRFLVIRADDPRCDILAAHTRYGHIVRGAKVIILVFLDREAmYNEVKDHQAAGAAVQNmLLAAHALQLGAVWLGEIINQAATLLPALALDPARLSFEAAIAAGHPAQNGSSSRRPLAELLLEEPFP 174
                                    12        22        32        42        52        62        72        82       |92       102    |  112       122       132       142       152       162       172  
                                                                                                                  90-MSE          107-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 3E39)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E39)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q314Q8_DESAG | Q314Q8)
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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