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(-) Description

Title :  THREE-DIMENSIONAL CRYSTAL STRUCTURE OF DISSIMILATORY SULFITE REDUCTASE D (DSRD)
 
Authors :  N. Mizuno, G. Voordouw, K. Miki, A. Sarai, Y. Higuchi
Date :  18 Apr 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Dissimilatory Sulfite Reductase D, Dna Binding Motif, Sulfate-Reducing Bacteria, Winged-Helix Motif, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Mizuno, G. Voordouw, K. Miki, A. Sarai, Y. Higuchi
Crystal Structure Of Dissimilatory Sulfite Reductase D (Dsrd) Protein-Possible Interaction With B- And Z-Dna By Its Winged-Helix Motif
Structure V. 11 1133 2003
PubMed-ID: 12962631  |  Reference-DOI: 10.1016/S0969-2126(03)00156-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DSVD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 881
    Synonym: DISSIMILATORY SULFITE REDUCTASE D, DSRD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:335 , HOH A:389 , LYS B:35 , GLN B:36 , ARG B:37 , HOH B:418BINDING SITE FOR RESIDUE SO4 B 201
2AC2SOFTWAREMET A:1 , GLU A:2 , LYS A:5 , HOH A:383 , HOH A:422BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREMET B:1 , GLU B:2 , LYS B:5BINDING SITE FOR RESIDUE SO4 B 203
4AC4SOFTWARESER A:56 , TYR B:23 , PHE B:24 , ASN B:25 , THR B:60 , THR B:61 , HOH B:456BINDING SITE FOR RESIDUE SO4 B 204
5AC5SOFTWARETYR A:23 , PHE A:24 , ASN A:25 , ASP A:26 , THR A:60 , THR A:61 , HOH A:322 , HOH A:331 , HOH A:375 , ASP B:29 , SER B:56BINDING SITE FOR RESIDUE SO4 A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UCR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UCR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UCR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UCR)

(-) Exons   (0, 0)

(no "Exon" information available for 1UCR)

(-) 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:74
 aligned with DSVD_DESVH | Q46582 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:74
                                    10        20        30        40        50        60        70    
            DSVD_DESVH    1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGKQAAA 74
               SCOP domains d1ucra_ A: Dissimilatory sulfite reductase DsvD                            SCOP domains
               CATH domains 1ucrA00 A:1-74 'winged helix' repressor DNA binding domain                 CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1ucr A  1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGKQAAA 74
                                    10        20        30        40        50        60        70    


Chain B from PDB  Type:PROTEIN  Length:75
 aligned with DSVD_DESVH | Q46582 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:75
                                    10        20        30        40        50        60        70     
            DSVD_DESVH    1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGKQAAAE 75
               SCOP domains d1ucrb_ B: Dissimilatory sulfite reductase DsvD                             SCOP domains
               CATH domains 1ucrB00 B:1-75 'winged helix' repressor DNA binding domain                  CATH domains
           Pfam domains (1) --DsrD-1ucrB01 B:3-69                                                ------ Pfam domains (1)
           Pfam domains (2) --DsrD-1ucrB02 B:3-69                                                ------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh........eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  1ucr B  1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGKQAAAE 75
                                    10        20        30        40        50        60        70
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DsrD] (2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1UCR)

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 Related Entries

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UniProtKB/Swiss-Prot
        DSVD_DESVH | Q46582: 1wq2

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