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(-) Description

Title :  CRYSTAL STRUCTURE OF ACIREDUCTONE DIOXYGENASE (13543033) FROM MUS MUSCULUS AT 2.06 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Jan 05  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A
Keywords :  13543033, Acireductone Dioxygenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, R. Schwarzenbacher, S. S. Krishna, D. Mcmullan, S. Agarwalla, K. Quijano, P. Abdubek, E. Ambing, H. Axelrod, T. Biorac, J. M. Canaves H. J. Chiu, M. A. Elsliger, C. Grittini, S. K. Grzechnik, M. Didonato, J. Hale, E. Hampton, G. W. Han, J. Haugen, M. Hornsby, L. Jaroszewski, H. E. Klock, M. W. Knuth, E. Koesema, A. Kreusch, P. Kuhn, M. D. Miller, K. Moy, E. Nigoghossian, J. Paulsen, R. Reyes, C. Rife, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, A. White, G. Wolf, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of Acireductone Dioxygenase (Ard) From Mu Musculus At 2. 06 Angstrom Resolution.
Proteins V. 64 808 2006
PubMed-ID: 16783794  |  Reference-DOI: 10.1002/PROT.20947

(-) Compounds

Molecule 1 - ACIREDUCTONE DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2MSE9Mod. Amino AcidSELENOMETHIONINE
3NI1Ligand/IonNICKEL (II) ION
4UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:88 , HIS A:90 , GLU A:94 , HIS A:133 , UNL A:201BINDING SITE FOR RESIDUE NI A 200
2AC2SOFTWAREPHE A:84 , HIS A:88 , HIS A:90 , GLU A:94 , ARG A:96 , HIS A:133 , ARG A:147 , NI A:200 , HOH A:235 , HOH A:365BINDING SITE FOR RESIDUE UNL A 201
3AC3SOFTWARELYS A:57 , ASN A:60 , ARG A:108 , HOH A:317BINDING SITE FOR RESIDUE IPA A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VR3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:21 -Pro A:22
2Arg A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VR3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VR3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VR3)

(-) 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:179
 aligned with MTND_MOUSE | Q99JT9 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           MTND_MOUSE     1 MVQAWYMDESTADPRKPHRAQPDRPVSLEQLRTLGVLYWKLDADKYENDPELEKIRKMRNYSWMDIITICKDTLPNYEEKIKMFFEEHLHLDEEIRYILEGSGYFDVRDKEDKWIRISMEKGDMITLPAGIYHRFTLDEKNYVKAMRLFVGEPVWTPYNRPADHFDARVQYMSFLEGTA 179
               SCOP domains d1vr3a1 A:1-179 Acireductone dioxygenase                                                                                                                                            SCOP domains
               CATH domains -1vr3A00 A:2-179 Jelly Rolls                                                                                                                                                        CATH domains
               Pfam domains --ARD-1vr3A01 A:3-157                                                                                                                                        ---------------------- Pfam domains
         Sec.struct. author ..eeee....................hhhhhhhh..eeee.hhhhh..hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.ee....eeeeeeeeeeeeeee.....eeeeeee..eeeee.....eeeee.....eeeeeee........ee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr3 A   1 mVQAWYmDESTADPRKPHRAQPDRPVSLEQLRTLGVLYWKLDADKYENDPELEKIRKmRNYSWmDIITICKDTLPNYEEKIKmFFEEHLHLDEEIRYILEGSGYFDVRDKEDKWIRISmEKGDmITLPAGIYHRFTLDEKNYVKAmRLFVGEPVWTPYNRPADHFDARVQYmSFLEGTA 179
                            |     | 10        20        30        40        50       |60   |    70        80  |     90       100       110       120   |   130       140     | 150       160       170 |       
                            |     7-MSE                                             58-MSE |                 83-MSE                             119-MSE|                   146-MSE                   172-MSE   
                            1-MSE                                                         64-MSE                                                     124-MSE
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTND_MOUSE | Q99JT9)
molecular function
    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: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: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:0006555    methionine metabolic process    The chemical reactions and pathways involving 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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTND_MOUSE | Q99JT9: 5i8s 5i8t 5i8y 5i91 5i93

(-) Related Entries Specified in the PDB File

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