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(-) Description

Title :  CRYSTAL STRUCTURE OF R138Q MUTANT 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 :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfite Oxidase; Molybdopterin; Molybdenum; Cso; Sulfate; R138Q; R160Q, 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
    Mutation: YES
    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  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MO2Ligand/IonMOLYBDENUM ATOM
3MTE2Ligand/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
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:138 , ARG A:190 , GLY A:201 , LEU A:202 , TRP A:204 , TYR A:322 , ARG A:450 , HOH A:7537 , HOH A:7631BINDING SITE FOR RESIDUE SO4 A 7503
2AC2SOFTWAREGLN B:138 , ARG B:190 , GLY B:201 , LEU B:202 , TRP B:204 , TYR B:322 , ARG B:450 , HOH B:9719 , HOH B:9756BINDING SITE FOR RESIDUE SO4 B 8503
3AC3SOFTWAREPHE A:135 , PHE A:136 , THR A:137 , GLN 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:7504 , HOH A:7505BINDING SITE FOR RESIDUE MTE A 1501
4AC4SOFTWARECYS A:185 , MTE A:1501 , HOH A:7504 , HOH A:7505BINDING SITE FOR RESIDUE MO A 2501
5AC5SOFTWAREPHE B:135 , PHE B:136 , THR B:137 , GLN 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:9506BINDING SITE FOR RESIDUE MTE B 4501
6AC6SOFTWARECYS B:185 , TYR B:322 , MTE B:4501 , HOH B:9506BINDING SITE FOR RESIDUE MO B 5501
7AC7SOFTWAREARG B:337 , THR B:338 , ALA B:339 , PRO B:340 , HOH B:9696BINDING SITE FOR RESIDUE GOL B 9505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A9C)

(-) 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 2A9C)

(-) 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 2A9C)

(-) 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: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 d2a9ca1 A:108-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                  d2a9ca2 A:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 2a9cA01 A:108-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                        2a9cA02 A:344-466  [code=2.60.40.650, no name defined]                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....ee..hhhhhh.....hhhhh.ee.............eeeee.....eeeeehhhhhhh..eeeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhh..........eeeeeeeee.....eeeeeeehhhhhh.....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
                 2a9c A 108 RVNSQKPFNAEPPAELLAERFLTPNELFFTQNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 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         


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 d2a9cb1 B:108-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                  d2a9cb2 B:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 2a9cB01 B:108-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                        2a9cB02 B:344-466  [code=2.60.40.650, no name defined]                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....ee..hhhhhh...........ee.............eeeee.....eeeeehhhhhhh...eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhh..........eeeeeeeee.....eeeeeeehhhhhh.....eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhh..............hhhhh........eeeeee....eee..eeeeeeeeee......eeeeeee......eee.ee.............eeeeeeeee....eeeeeeeeee.........hhhhh..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------MOLYBDOPTERIN_EUK  PDB: B:157-192   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9c B 108 RVNSQKPFNAEPPAELLAERFLTPNELFFTQNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 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 2A9C)

(-) 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.

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  2a9c
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  1.8.3.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SUOX_CHICK | P07850: 1sox 2a99 2a9a 2a9b 2a9d 3hbg 3hbp 3hbq 3r18 3r19

(-) Related Entries Specified in the PDB File

2a99 WILD TYPE ENZYME AT RESTING STATE
2a9a WILD TYPE ENZYME WITH THE BOUND PRODUCT
2a9b R138Q MUTANT AT RESTING STATE
2a9d SAME PROTEIN WITH AN ARG AT RESIDUE 161