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(-) Description

Title :  SULFITE DEHYDROGENASE FROM STARKEYA NOVELLA
 
Authors :  S. Bailey, U. Kappler
Date :  19 Apr 05  (Deposition) - 28 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfite Oxidase, Molybdopterin, C-Type Cytochrome, Heme, Electron Transport, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Kappler, S. Bailey
Molecular Basis Of Intramolecular Electron Transfer In Sulfite-Oxidizing Enzymes Is Revealed By High Resolution Structure Of A Heterodimeric Complex Of The Catalytic Molybdopterin Subunit And A C-Type Cytochrome Subunit.
J. Biol. Chem. V. 280 24999 2005
PubMed-ID: 15863498  |  Reference-DOI: 10.1074/JBC.M503237200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFITE:CYTOCHROME C OXIDOREDUCTASE SUBUNIT A
    Chains: A
    Engineered: YES
    Expression System: RHODOBACTER CAPSULATUS
    Expression System Taxid: 1061
    Organism Scientific: STARKEYA NOVELLA
    Organism Taxid: 921
    Synonym: SORA
 
Molecule 2 - SULFITE:CYTOCHROME C OXIDOREDUCTASE SUBUNIT B
    Chains: B
    Engineered: YES
    Expression System: RHODOBACTER CAPSULATUS
    Expression System Taxid: 1061
    Organism Scientific: STARKEYA NOVELLA
    Organism Taxid: 921
    Synonym: SORB

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2MSS1Ligand/Ion(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:53 , VAL A:54 , ARG A:55 , TYR A:56 , HIS A:57 , ASN A:102 , CYS A:104 , SER A:105 , ASP A:158 , PHE A:168 , ASN A:197 , ARG A:202 , GLY A:210 , THR A:211 , TRP A:213 , LYS A:215 , TYR A:236 , HOH A:2278BINDING SITE FOR RESIDUE MSS A1374
2AC2SOFTWAREGLN A:33 , ARG A:55 , TYR A:56 , HIS A:57 , ASN B:528 , CYS B:529 , CYS B:532 , HIS B:533 , TYR B:537 , ILE B:538 , GLN B:541 , GLU B:553 , LYS B:556 , MET B:557 , TYR B:561 , ALA B:563 , LEU B:577 , HOH B:2063 , HOH B:2083BINDING SITE FOR RESIDUE HEC B1582

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:243 -A:245

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:30 -Pro A:31
2Glu A:113 -Pro A:114
3Tyr A:199 -Pro A:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BPB)

(-) Exons   (0, 0)

(no "Exon" information available for 2BPB)

(-) 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:373
 aligned with Q9LA16_STANO | Q9LA16 from UniProtKB/TrEMBL  Length:405

    Alignment length:373
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   
         Q9LA16_STANO    33 ADTVTLPFANGERPLVMYPGKRPLIGLTARPPQLETPFSVFDEGLITPNDAFFVRYHLAGIPLEIDPDAFRLEIKGKVGTPLSLSLQDLKNDFPASEVVAVNQCSGNSRGFVEPRVGGGQLANGAMGNARWRGVPLKAVLEKAGVQAGAKQVTFGGLDGPVIPETPDFVKALSIDHATDGEVMLAYSMNGADLPWLNGYPLRLVVPGYYGTYWVKHLNEITVIDKEFDGFWMKTAYRIPDNACACTEPGKAPTATIPINRFDVRSFITNVENGASVKAGEVPLRGIAFDGGYGITQVSVSADAGKSWTNATLDPGLGKYSFRGWKAVLPLTKGDHVLMCRATNARGETQPMQATWNPAGYMRNVVEATRVIAA 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......eeeee.......eeeee....eee.hhhhhhh....hhhhh.ee........ee......eeeee.....eeehhhhhhhhh..eeeeeeee....hhhhh.............eeeeeeeeeehhhhhhhhh......eeeeee............eeeeehhhhh....eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhh..eee...............eee......eeee......eeee.eeeeeeeeee.....eeeeeee.......ee.ee.........eeeeeeeee..eeeeeeeeeee......................eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpb A   1 ADTVTLPFANGERPLVMYPGKRPLIGLTARPPQLETPFSVFDEGLITPNDAFFVRYHLAGIPLEIDPDAFRLEIKGKVGTPLSLSLQDLKNDFPASEVVAVNQCSGNSRGFVEPRVGGGQLANGAMGNARWRGVPLKAVLEKAGVQAGAKQVTFGGLDGPVIPETPDFVKALSIDHATDGEVMLAYSMNGADLPWLNGYPLRLVVPGYYGTYWVKHLNEITVIDKEFDGFWMKTAYRIPDNACACTEPGKAPTATIPINRFDVRSFITNVENGASVKAGEVPLRGIAFDGGYGITQVSVSADAGKSWTNATLDPGLGKYSFRGWKAVLPLTKGDHVLMCRATNARGETQPMQATWNPAGYMRNVVEATRVIAA 373
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370   


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with Q9LA15_STANO | Q9LA15 from UniProtKB/TrEMBL  Length:108

    Alignment length:81
                                    37        47        57        67        77        87        97       107 
         Q9LA15_STANO    28 APLTYELPDETAQLKPAPQPGFEAAQNNCAACHSVDYINTQPPGKGQAFWDAEVQKMIKVYHAPVDEADAKAIADYLAKTY 108
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...............hhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2bpb B 501 APLTYELPDETAQLKPAPQPGFEAAQNNCAACHSVDYINTQPPGKGQAFWDAEVQKMIKVYHAPVDEADAKAIADYLAKTY 581
                                   510       520       530       540       550       560       570       580
   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  (0, 0)

(no "SCOP Domain" information available for 2BPB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BPB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9LA16_STANO | Q9LA16)
molecular function
    GO:0030151    molybdenum ion binding    Interacting selectively and non-covalently with molybdenum (Mo) ions.
    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: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.

Chain B   (Q9LA15_STANO | Q9LA15)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9LA15_STANO | Q9LA15: 2blf 2c9x 2ca3 2ca4
        Q9LA16_STANO | Q9LA16: 2blf 2c9x 2ca3 2ca4

(-) Related Entries Specified in the PDB File

2blf SULFITE DEHYDROGENASE FROM STARKEYA NOVELLA