Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT CHICKEN SULFITE OXIDASE WITH THE BOUND PRODUCT, SULFATE, AT THE ACTIVE SITE
 
Authors :  E. Karakas, H. L. Wilson, T. N. Graf, S. Xiang, S. Jaramillo-Busquets, K. V. Rajagopalan, C. Kisker
Date :  11 Jul 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfite Oxidase; Molybdopterin; Molybdenum, Cso; Sulfate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Karakas, H. L. Wilson, T. N. Graf, S. Xiang, S. Jaramillo-Busquets, K. V. Rajagopalan, C. Kisker
Structural Insights Into Sulfite Oxidase Deficiency
J. Biol. Chem. V. 280 33506 2005
PubMed-ID: 16048997  |  Reference-DOI: 10.1074/JBC.M505035200

(-) Compounds

Molecule 1 - SULFITE OXIDASE
    Cellular Location: MITOCHONDRIAL INTERMEMBRANE SPACE
    Chains: A, B
    EC Number: 1.8.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: TP1000
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC CORE DOMAIN AND C TERMINAL DIMERIZATION DOMAIN
    Gene: SUOX
    Organ: LIVER
    Organelle: MITOCHONDRION
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Other Details: THE GENE IS CHEMICALLY SYNTHESIZED BASED ON THE PROTEIN SEQUENCE OF SULFITE OXIDASE FROM GALLUS GALLUS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MO2Ligand/IonMOLYBDENUM ATOM
2MTE2Ligand/IonPHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
3SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:138 , CYS A:185 , ARG A:190 , LEU A:202 , TRP A:204 , TYR A:322 , ARG A:450 , HOH A:7506 , HOH A:7600BINDING SITE FOR RESIDUE SO4 A 7503
2AC2SOFTWAREHIS A:140 , TRP A:317 , HOH A:7573 , HOH A:7602 , HOH A:7759 , ARG B:337BINDING SITE FOR RESIDUE SO4 A 7504
3AC3SOFTWAREARG B:138 , CYS B:185 , ARG B:190 , GLY B:201 , LEU B:202 , TRP B:204 , TYR B:322 , ARG B:450 , HOH B:8506 , HOH B:8678BINDING SITE FOR RESIDUE SO4 B 8503
4AC4SOFTWAREARG A:337 , TRP B:317 , HOH B:8595 , HOH B:8750BINDING SITE FOR RESIDUE SO4 B 8504
5AC5SOFTWAREPHE A:135 , PHE A:136 , THR A:137 , ARG A:138 , HIS A:140 , CYS A:185 , ASP A:244 , TYR A:252 , HIS A:283 , ARG A:288 , GLY A:296 , ALA A:297 , SER A:299 , VAL A:300 , LYS A:301 , TRP A:302 , TYR A:322 , MO A:2501 , HOH A:7506BINDING SITE FOR RESIDUE MTE A 1501
6AC6SOFTWARECYS A:185 , MTE A:1501 , HOH A:7505 , HOH A:7506BINDING SITE FOR RESIDUE MO A 2501
7AC7SOFTWAREPHE B:135 , PHE B:136 , THR B:137 , ARG B:138 , HIS B:140 , CYS B:185 , ASP B:244 , TYR B:252 , HIS B:283 , ARG B:288 , GLY B:296 , ALA B:297 , SER B:299 , VAL B:300 , LYS B:301 , TRP B:302 , TYR B:322 , MO B:5501 , HOH B:8506BINDING SITE FOR RESIDUE MTE B 4501
8AC8SOFTWARECYS B:185 , MTE B:4501 , HOH B:8505 , HOH B:8506BINDING SITE FOR RESIDUE MO B 5501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A9A)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Lys A:113 -Pro A:114
2Phe A:285 -Pro A:286
3Gln A:353 -Pro A:354
4Lys B:113 -Pro B:114
5Phe B:285 -Pro B:286
6Gln B:353 -Pro B:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A9A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOLYBDOPTERIN_EUKPS00559 Eukaryotic molybdopterin oxidoreductases signature.SUOX_CHICK157-192
 		  2A:157-192
B:157-192

(-) Exons   (0, 0)

(no "Exon" information available for 2A9A)

(-) 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:371
 aligned with SUOX_CHICK | P07850 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:371
                                                                                                                                                                                                                                                                                                                                                                                                     459       
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455   |     - 
           SUOX_CHICK    96 PFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGRTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGASLRDVLLHAGFPEELQGGEHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHRFPVRVVVPGVVGARSVKWLRRVAVSPDESPSRWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHR-------   -
               SCOP domains d2a9aa2 A:96-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                               d2a9aa1 A:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 2a9aA01 A:96-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                                     2a9aA02 A:344-466  [code=2.60.40.650, no name defined]                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....eee.hhhhhh...........ee..............eeee.....eeeehhhhhhhhh..eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhh..........eeeeeeeee.....eeeeeeehhhhhhhhhh.eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhh..............hhhhh........eeeeee.....ee..eeeeeeeeee......eeeeeee.......ee.eee............eeeeeeeee....eeeeeeeeee.........hhhhh..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------MOLYBDOPTERIN_EUK  PDB: A:157-192   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9a A  96 PFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 466
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465 


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with SUOX_CHICK | P07850 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:359
                                                                                                                                                                                                                                                                                                                                                                                         459       
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457 |       
           SUOX_CHICK   108 RVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGRTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGASLRDVLLHAGFPEELQGGEHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHRFPVRVVVPGVVGARSVKWLRRVAVSPDESPSRWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHR-------   -
               SCOP domains d2a9ab1 B:108-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                  d2a9ab2 B:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 2a9aB01 B:108-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                        2a9aB02 B:344-466  [code=2.60.40.650, no name defined]                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....ee..hhhhhh...........ee..............eeee......eeehhhhhhhhh..eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhh..........eeeeeeeee.....eeeeeeehhhhhhhhhh.eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhh..............hhhhh........eeeeee.....ee..eeeeeeeeee......eeeeeee.......ee.eee............eeeeeeeee....eeeeeeeeee.........hhhhh..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------MOLYBDOPTERIN_EUK  PDB: B:157-192   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9a B 108 RVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 466
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A9A)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SUOX_CHICK | P07850)
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: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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MTE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:353 - Pro A:354   [ RasMol ]  
    Gln B:353 - Pro B:354   [ RasMol ]  
    Lys A:113 - Pro A:114   [ RasMol ]  
    Lys B:113 - Pro B:114   [ RasMol ]  
    Phe A:285 - Pro A:286   [ RasMol ]  
    Phe B:285 - Pro B:286   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2a9a
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SUOX_CHICK | P07850
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.8.3.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SUOX_CHICK | P07850
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SUOX_CHICK | P07850: 1sox 2a99 2a9b 2a9c 2a9d 3hbg 3hbp 3hbq 3r18 3r19

(-) Related Entries Specified in the PDB File

2a99 WILD TYPE ENZYME AT RESTING STATE
2a9b R138Q MUTANT AT RESTING STATE
2a9c R138Q MUTANT WITH THE BOUND PRODUCT
2a9d SAME PROTEIN WITH AN ARG AT RESIDUE 161