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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE MYO-INOSITOL OXYGENASE (RE-REFINED)
 
Authors :  B. M. Hallberg
Date :  13 Jan 08  (Deposition) - 05 Feb 08  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Substrate Complex, Hd Domain Fold, Diiron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Thorsell, C. Persson, N. Voevodskaya, R. D. Busam, M. Hammarstrom, S. Graslund, A. Graslund, B. M. Hallberg
Structural And Biophysical Characterization Of Human Myo-Inositol Oxygenase.
J. Biol. Chem. V. 283 15209 2008
PubMed-ID: 18364358  |  Reference-DOI: 10.1074/JBC.M800348200

(-) Compounds

Molecule 1 - INOSITOL OXYGENASE
    Chains: A
    EC Number: 1.13.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPRO EX HTB
    Expression System Strain: BL21 (DE3) PRP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MUS MUSCULUS MYO-INOSITOL OXYGENASE
    Gene: MIOX, ALDRL6, RSOR
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MYO-INOSITOL OXYGENASE, ALDEHYDE REDUCTASE-LIKE 6, RENAL- SPECIFIC OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2FMT1Ligand/IonFORMIC ACID
3INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
4OH1Ligand/IonHYDROXIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:98 , HIS A:123 , ASP A:124 , ASP A:253 , FE A:302 , INS A:303 , OH A:304 , HOH A:310BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREASP A:124 , HIS A:194 , HIS A:220 , FE A:301 , INS A:303 , OH A:304BINDING SITE FOR RESIDUE FE A 302
3AC3SOFTWAREHIS A:123 , ASP A:124 , HIS A:220 , ASP A:253 , FE A:301 , FE A:302 , INS A:303BINDING SITE FOR RESIDUE OH A 304
4AC4SOFTWAREARG A:29 , TYR A:44 , ASP A:85 , SER A:87 , ASP A:88 , ASP A:124 , LYS A:127 , GLY A:141 , ASP A:142 , HIS A:194 , HIS A:220 , SER A:221 , TYR A:223 , FE A:301 , FE A:302 , OH A:304 , HOH A:386BINDING SITE FOR RESIDUE INS A 303
5AC5SOFTWAREVAL A:146 , GLY A:147 , CYS A:148 , ASN A:164 , ASP A:166BINDING SITE FOR RESIDUE FMT A 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BXD)

(-) 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:258
 aligned with MIOX_MOUSE | Q9QXN5 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:258
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277        
           MIOX_MOUSE    28 FRNYTSGPLLDRVFTTYKLMHTHQTVDFVSRKRIQYGSFSYKKMTIMEAVGMLDDLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKIMALWGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLENVLMSWGHDEYLYQMMKFNKFSLPSEAFYMIRFHSFYPWHTGGDYRQLCSQQDLDMLPWVQEFNKFDLYTKCPDLPDVESLRPYYQGLIDKYCPGTLSW 285
               SCOP domains d3bxda_ A: Myo-inositol oxygenase MioX                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eehhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhh................hhhhh...hhhhhh..............hhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bxd A  28 FRNYTSGPLLDRVFTTYKLMHTHQTVDFVSRKRIQYGSFSYKKMTIMEAVGMLDDLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKIMALWGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLENVLMSWGHDEYLYQMMKFNKFSLPSEAFYMIRFHSFYPWHTGGDYRQLCSQQDLDMLPWVQEFNKFDLYTKCPDLPDVESLRPYYQGLIDKYCPGTLSW 285
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MIOX_MOUSE | Q9QXN5)
molecular function
    GO:0004033    aldo-keto reductase (NADP) activity    Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0050113    inositol oxygenase activity    Catalysis of the reaction: myo-inositol + O(2) = D-glucuronate + H(2)O + H(+).
    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.
    GO:0016651    oxidoreductase activity, acting on NAD(P)H    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0016701    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor.
biological process
    GO:0019310    inositol catabolic process    The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016234    inclusion body    A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers.

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  3bxd
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  MIOX_MOUSE | Q9QXN5
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 Related Entries

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

UniProtKB/Swiss-Prot
        MIOX_MOUSE | Q9QXN5: 2huo

(-) Related Entries Specified in the PDB File

2huo THIS WAS THE STARTING MODEL FOR A RE-REFINEMENT MOSTLY INVOLVING THE FIRST N-TERMINAL RESIDUES BUT ALSO INVOLVING A REBUILD OF THE WATER MODEL AND CHANGE OF ROTAMERS TO BETTER CORRESPOND TO THEIR MOST PROBABLE CONFORMATION (PROTEINS. 2000 AUG 15;40(3):389-408. THE PENULTIMATE ROTAMER LIBRARY. LOVELL SC, WORD JM, RICHARDSON JS, RICHARDSON DC.) EXPERIMENTAL DATA FROM 2HUO, BUT ANISOTROPICALLY CORRECTED ACCORDING TO M. STRONG, M.R. SAWAYA, S. WANG, M. PHILLIPS, D. CASCIO, D. EISENBERG, PROC.NATL.ACAD.SCI.USA. 103, 8060-65, 2006.