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(-) Description

Title :  CRYSAL STRUCTURE OF THE MIMIVIRUS SULFHYDRYL OXIDASE R596
 
Authors :  M. Hakim, D. Fass
Date :  10 Aug 11  (Deposition) - 05 Sep 12  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Four Helix-Bundle, Orfan Domain, Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hakim, D. Ezerina, A. Alon, O. Vonshak, D. Fass
Exploring Orfan Domains In Giant Viruses: Structure Of Mimivirus Sulfhydryl Oxidase R596.
Plos One V. 7 50649 2012
PubMed-ID: 23209798  |  Reference-DOI: 10.1371/JOURNAL.PONE.0050649

(-) Compounds

Molecule 1 - FAD-LINKED SULFHYDRYL OXIDASE R596
    Chains: A
    EC Number: 1.8.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MIMI_R596, R596
    Mutation: YES
    Organism Common: APMV
    Organism Scientific: ACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid: 212035

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:37 , TRP A:40 , GLY A:41 , THR A:42 , GLY A:44 , TRP A:45 , HIS A:49 , CYS A:83 , TYR A:114 , HIS A:117 , ASN A:118 , VAL A:120 , ASN A:121 , LYS A:123 , LEU A:124 , TYR A:128 , LEU A:130 , VAL A:135 , LYS A:138 , ASP A:174 , ARG A:237 , HOH A:296 , HOH A:299 , HOH A:300 , HOH A:332 , HOH A:336 , HOH A:337 , HOH A:344 , HOH A:369BINDING SITE FOR RESIDUE FAD A 334

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:80 -A:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TD7)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.YR596_MIMIV33-139  1A:33-139
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.YR596_MIMIV33-139  2A:33-139

(-) Exons   (0, 0)

(no "Exon" information available for 3TD7)

(-) Sequences/Alignments

Asymmetric 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:253
 aligned with YR596_MIMIV | Q5UP54 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:261
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
          YR596_MIMIV    32 HNGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRAKCGKPVPTVKGCVTPLDHKAFSFKKLYYMDAPIVSLDKVENFVRIARMRGISDKYFCFLELATVLNGDFNELKKQSSWEYRNKYCQKKIRHMRENAIPSIEEQGYWKGTPTIDELKLLLFLCSNLNRTEVNDAINNVERLESTHYIEN 292
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......--------..hhhhhhhhhhhhhh......hhhhhh.hhhhhhhh..hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ERV_ALR  PDB: A:33-139 UniProt: 33-139                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td7 A  32 HNGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRAKCGK--------VTPLDHKAFSFKKLYYMDAPIVSLDKVENFVRIARMRGISDKYFAFLELATVLNGDFNELKKQSSWEYRNKYAQKKIRHMRENAIPSIEEQGYWKGTPTIDELKLLLFLASNLNRTEVNDAINNVERLESTHYIEN 292
                                    41        51        61        71        81        91       101       111       121       131       141      |  -     | 161       171       181       191       201       211       221       231       241       251       261       271       281       291 
                                                                                                                                              148      157
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3TD7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TD7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TD7)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (YR596_MIMIV | Q5UP54)
molecular function
    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:0016972    thiol oxidase activity    Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O.
biological process
    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:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YR596_MIMIV | Q5UP54: 3gwn

(-) Related Entries Specified in the PDB File

3gwl HOMOLOG FROM AFRICAN SWINE FEVER VIRUS
3gwn TRUNCATED VERSION OF THIS PROTEIN, INCLUDES ONLY THE ERV SULFHYDRYL OXIDASE DOMAIN
3p0k HOMOLOG FROM BACULOVIRUS