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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE CYTOCHROME B5 DOMAIN OF HUMAN SULFITE OXIDASE
 
Authors :  M. J. Rudolph, J. L. Johnson, K. V. Rajagopalan, C. Kisker
Date :  26 Aug 02  (Deposition) - 12 Sep 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome B5, Heme, Sulfite Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Rudolph, J. L. Johnson, K. V. Rajagopalan, C. Kisker
The 1. 2 A Structure Of The Human Sulfite Oxidase Cytochrome B(5) Domain.
Acta Crystallogr. , Sect. D V. 59 1183 2003
PubMed-ID: 12832761  |  Reference-DOI: 10.1107/S0907444903009934

(-) Compounds

Molecule 1 - SULFITE OXIDASE
    Chains: A
    EC Number: 1.8.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CYTOCHROME B5 DOMAIN, RESIDUES 22-103 OF SWS P51687
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:46 , GLN A:67 , SER A:68 , HOH A:510 , HOH A:525 , HOH A:527 , HOH A:577 , HOH A:596BINDING SITE FOR RESIDUE SO4 A 83
2AC2SOFTWAREHIS A:40 , PRO A:41 , LYS A:46 , LEU A:47 , TRP A:59 , TYR A:62 , HIS A:65 , GLN A:67 , HIS A:69 , HOH A:539 , HOH A:546 , HOH A:573 , HOH A:584 , GOL A:9601BINDING SITE FOR RESIDUE HEM A 502
3AC3SOFTWAREPRO A:41 , HIS A:69 , ARG A:71 , HEM A:502 , HOH A:513 , HOH A:518 , HOH A:530 , HOH A:531BINDING SITE FOR RESIDUE GOL A 9601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MJ4)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.SUOX_HUMAN82-161  1A:4-82
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.SUOX_HUMAN114-121  1A:36-43

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003941151ENSE00001481719chr12:56391043-5639112381SUOX_HUMAN-00--
1.2ENST000003941152ENSE00001401006chr12:56391399-56391507109SUOX_HUMAN-00--
1.3ENST000003941153ENSE00001517532chr12:56393117-56393242126SUOX_HUMAN-00--
1.4bENST000003941154bENSE00001517529chr12:56395996-5639605560SUOX_HUMAN1-17170--
1.5ENST000003941155ENSE00001481715chr12:56396327-56396504178SUOX_HUMAN17-76600--
1.6aENST000003941156aENSE00001425993chr12:56397402-563993051904SUOX_HUMAN77-5454691A:3-8280

(-) 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:80
 aligned with SUOX_HUMAN | P51687 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:80
                                    90       100       110       120       130       140       150       160
           SUOX_HUMAN    81 STHIYTKEEVSSHTSPETGIWVTLGSEVFDVTEFVDLHPGGPSKLMLAAGGPLEPFWALYAVHNQSHVRELLAQYKIGEL 160
               SCOP domains d1mj4a_ A: Sulfite oxidase, N-terminal domain                                    SCOP domains
               CATH domains 1mj4A00 A:3-82 Flavocytochrome B2, subunit A, domain 1                           CATH domains
               Pfam domains ---Cyt-b5-1mj4A01 A:6-82                                                         Pfam domains
         Sec.struct. author .....hhhhhhh.ee...eeeeee..eeee...hhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYTOCHROME_B5_2  PDB: A:4-82 UniProt: 82-161                                    PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.6a  PDB: A:3-82 UniProt: 77-545 [INCOMPLETE]                              Transcript 1
                 1mj4 A   3 STHIYTKEEVSSHTSPETGIWVTLGSEVFDVTEFVDLHPGGPSKLMLAAGGPLEPFWALYAVHNQSHVRELLAQYKIGEL  82
                                    12        22        32        42        52        62        72        82
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Cyt-b5] (29)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUOX_HUMAN | P51687)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030151    molybdenum ion binding    Interacting selectively and non-covalently with molybdenum (Mo) ions.
    GO:0043546    molybdopterin cofactor binding    Interacting selectively and non-covalently with the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
    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:0008482    sulfite oxidase activity    Catalysis of the reaction: H(2)O + O(2) + sulfite = H(2)O(2) + H(+) + sulfate.
biological process
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    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.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0070221    sulfide oxidation, using sulfide:quinone oxidoreductase    A sulfide oxidation process that proceeds via the reaction catalyzed by sulfide:quinone oxidoreductase.
    GO:0006790    sulfur compound metabolic process    The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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1sox SULFITE OXIDASE FROM CHICKEN LIVER