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(-) Description

Title :  RESIDUAL DIPOLAR COUPLING REFINEMENT OF ACIREDUCTONE DIOXYGENASE FROM KLEBSIELLA
 
Authors :  T. C. Pochapsky, S. S. Pochapsky, T. Ju, C. Hoefler, J. Liang
Date :  19 May 05  (Deposition) - 06 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (17x)
Keywords :  Nickel, Cupin, Beta Helix, Methionine Salvage, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Pochapsky, S. S. Pochapsky, T. Ju, C. Hoefler, J. Liang
A Refined Model For The Structure Of Acireductone Dioxygenase From Klebsiella Atcc 8724 Incorporating Residual Dipolar Couplings
J. Biomol. Nmr V. 34 117 2006
PubMed-ID: 16518698  |  Reference-DOI: 10.1007/S10858-005-5735-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E-2/E-2' PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: KLEBSIELLA OXYTOCA
    Organism Taxid: 571

 Structural Features

(-) Chains, Units

  
NMR Structure (17x): 

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
1AC1SOFTWAREHIS A:96 , HIS A:98 , GLU A:102 , HIS A:140 , HOH A:181 , HOH A:182BINDING SITE FOR RESIDUE NI A 180

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZRR)

(-) 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:179
 aligned with MTND_KLEOX | Q9ZFE7 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           MTND_KLEOX     2 SALTIFSVKDPQNSLWHSTNAEEIQQQLNAKGVRFERWQADRDLGAAPTAETVIAAYQHAIDKLVAEKGYQSWDVISLRADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIAQFTGDDIASAYPRLA 180
               SCOP domains d1zrra_ A: Acireductone dioxygenase                                                                                                                                                 SCOP domains
               CATH domains 1zrrA00 A:1-179 Jelly Rolls                                                                                                                                                         CATH domains
               Pfam domains --ARD-1zrrA01 A:3-164                                                                                                                                               --------------- Pfam domains
         Sec.struct. author .eeeee.......eeeee..hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh..ee...eeeeeee......ee....eeeee.....eeee................eeeeee.hhh.ee.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zrr A   1 SALTIFSVKDPQNSLWHSTNAEEIQQQLNAKGVRFERWQADRDLGAAPTAETVIAAYQHAIDKLVAEKGYQSWDVISLRADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIAQFTGDDIASAYPRLA 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Cupin (179)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (MTND_KLEOX | Q9ZFE7)
molecular function
    GO:0010308    acireductone dioxygenase (Ni2+-requiring) activity    Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 3-(methylthio)propanoate + CO + formate.
    GO:0010309    acireductone dioxygenase [iron(II)-requiring] activity    Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 4-methylthio-2-oxobutanoate + formate + H(+).
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    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:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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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        MTND_KLEOX | Q9ZFE7: 2hji

(-) Related Entries Specified in the PDB File

1m4o NMR STRUCTURE OF ACIREDUCTONE DIOXYGENASE FROM KLEBSIELLA