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(-) Description

Title :  NMR STRUCTURE OF NI SUBSTITUED DESULFOVIBRIO VULGARIS RUBREDOXIN
 
Authors :  S. G. Nunes, B. F. Volkman, J. J. G. Moura, I. Moura, A. L. Macedo, J. L. Markley, I. C. Duarte
Date :  18 Jun 09  (Deposition) - 22 Dec 09  (Release) - 16 Mar 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Electron Transport, [Fe-4S], Iron, Metal-Binding, Cytoplasm, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Goodfellow, I. C. Duarte, A. L. Macedo, B. F. Volkman, S. G. Nunes, I. Moura, J. L. Markley, J. J. Moura
An Nmr Structural Study Of Nickel-Substituted Rubredoxin
J. Biol. Inorg. Chem. V. 15 409 2010
PubMed-ID: 19997764  |  Reference-DOI: 10.1007/S00775-009-0613-6

(-) Compounds

Molecule 1 - RUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PT7-7
    Gene: RUB, DVU_3184
    Organism Scientific: DESULFOVIBRIO VULGARIS STR. HILDENBOROUGH
    Organism Taxid: 882
    Strain: HIDENBOROUGH/ATCC 29579/NCIMB 8303
    Synonym: RD

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , CYS A:9 , CYS A:39 , CYS A:42 , ALA A:44BINDING SITE FOR RESIDUE NI A 53

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR_DESVH1-52  1A:1-52
2RUBREDOXINPS00202 Rubredoxin signature.RUBR_DESVH33-43  1A:33-43

(-) Exons   (0, 0)

(no "Exon" information available for 2KKD)

(-) Sequences/Alignments

NMR Structure
   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:52
 aligned with RUBR_DESVH | P00269 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:52
                                    10        20        30        40        50  
            RUBR_DESVH    1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA 52
               SCOP domains d2kkda_ A: Rubredoxin                                SCOP domains
               CATH domains 2kkdA00 A:1-52  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains --Rubredoxin-2kkdA01 A:3-49                      --- Pfam domains
         Sec.struct. author ....ee......................hhhhh...........hhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52           PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  2kkd A  1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA 52
                                    10        20        30        40        50
   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, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Rubredoxin (46)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (RUBR_DESVH | P00269)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  RUBR_DESVH | P00269
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUBR_DESVH | P00269: 1rb9 2ql0 7rxn 8rxn

(-) Related Entries Specified in the PDB File

2ql0 NMR STUCTURE OF THE ZN SUBSTITUTED FORM OF THE SAME PROTEIN
8rxn X-RAY STUCTURE OF SAME PROTEIN BUT WITH NATIVE FE CENTRE