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(-) Description

Title :  CRYSTAL STRUCTURE OF A NITROREDUCTASE FAMILY PROTEIN (CD3355) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Apr 09  (Deposition) - 19 May 09  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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 Nitroreductase Family Protein (Yp_001089872. 1) From Clostridium Difficile 630 At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITROREDUCTASE FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CD3355, YP_001089872.1
    Organism Scientific: CLOSTRIDIUM DIFFICILE 630
    Organism Taxid: 272563

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , SER A:12 , ARG A:14 , PRO A:37 , THR A:38 , GLY A:39 , ASN A:41 , TYR A:66 , ILE A:94 , ASP A:95 , ILE A:98 , VAL A:115 , TRP A:116 , VAL A:117 , CYS A:118 , TYR A:119 , GLU A:151 , ARG A:155 , ARG A:160 , MPD A:173 , HOH A:305 , HOH A:320 , HOH A:328 , HOH A:345BINDING SITE FOR RESIDUE FMN A 300
2AC2SOFTWAREGLY A:40 , TRP A:82 , HOH A:272 , FMN A:300BINDING SITE FOR RESIDUE MPD A 173
3AC3SOFTWAREALA A:62 , ALA A:63 , PHE A:86 , TYR A:119 , HOH A:282 , HOH A:324 , HOH A:396BINDING SITE FOR RESIDUE MRD A 174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H4O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H4O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H4O)

(-) Exons   (0, 0)

(no "Exon" information available for 3H4O)

(-) 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:172
 aligned with Q180K0_PEPD6 | Q180K0 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q180K0_PEPD6     1 MNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL 172
               SCOP domains d3h4oa_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhh......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh.....eeeeeeeeee..........hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4o A   1 mNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHmmLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLmGYESKIPESPERHEKTRVPLSEIVSYETL 172
                            |       10        20        30        40        50        60        70        80        90       100  ||   110       120       130       140  |    150       160       170  
                            |                                                                                                   103-MSE                                 143-MSE                         
                            1-MSE                                                                                                104-MSE
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H4O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H4O)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q180K0_PEPD6 | Q180K0)
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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 Related Entries

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UniProtKB/TrEMBL
        Q180K0_PEPD6 | Q180K0: 3koq

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