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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE FAD BINDING DOMAIN FROM MIMIVIRUS SULFHYDRYL OXIDASE R596

Authors :   M. Hakim, D. Fass

Date :   01 Apr 09 (Deposition) - 07 Jul 09 (Release) - 07 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym./Biol. Unit : A,B

Keywords :   Five Helix Bundle, Homodimer, Disulfide Bond, Fad, Flavoprotein, Oxidoreductase, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hakim, D. Fass
Dimer Interface Migration In A Viral Sulfhydryl Oxidase
J. Mol. Biol. V. 391 758 2009
PubMed-ID: 19576902 | Reference-DOI: 10.1016/J.JMB.2009.06.070

Molecule 1 - PROBABLE FAD-LINKED SULFHYDRYL OXIDASE R596
	Chains	:	A, B
	EC Number	:	1.8.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	MIMIVIRUS R596 FAD BINDING DOMAIN
	Gene	:	MIMI_R596, R596
	Organism Common	:	APMV
	Organism Scientific	:	ACANTHAMOEBA POLYPHAGA MIMIVIRUS
	Organism Taxid	:	212035

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:24 , HOH A:27 , HOH A:28 , HOH A:29 , THR A:37 , TRP A:40 , GLY A:41 , THR A:42 , TRP A:45 , HIS A:49 , SER A:61 , LEU A:78 , CYS A:83 , LYS A:89 , THR A:92 , THR A:93 , TYR A:114 , HIS A:117 , ASN A:118 , ASN A:121 , LEU A:124 , TYR A:128 , LEU A:130 , VAL A:135 , HOH A:168 , HOH A:179 , HOH A:202 , HOH A:217 , HOH A:233	BINDING SITE FOR RESIDUE FAD A 334
2	AC2	SOFTWARE	THR A:60 , SER A:61 , LYS A:138 , HOH A:166 , HOH A:175 , HOH A:182	BINDING SITE FOR RESIDUE SO4 A 1
3	AC3	SOFTWARE	ARG A:65 , ARG A:66 , HOH A:240 , HOH B:243	BINDING SITE FOR RESIDUE SO4 A 2
4	AC4	SOFTWARE	ASP A:76 , ARG A:84 , GLU A:125 , GLY B:54 , PRO B:56 , ASP B:63 , TYR B:67 , HOH B:159 , HOH B:186 , HOH B:190	BINDING SITE FOR RESIDUE GOL B 1
5	AC5	SOFTWARE	HOH B:10 , THR B:37 , TRP B:40 , GLY B:41 , THR B:42 , TRP B:45 , HIS B:49 , CYS B:83 , SER B:86 , TYR B:114 , HIS B:117 , ASN B:118 , VAL B:120 , ASN B:121 , TYR B:128 , LEU B:130 , VAL B:135 , HOH B:160 , HOH B:163 , HOH B:179 , HOH B:180 , HOH B:182 , HOH B:183 , HOH B:193 , HOH B:230 , HOH B:237	BINDING SITE FOR RESIDUE FAD B 335
6	AC6	SOFTWARE	SER B:131 , TYR B:132 , GLU B:133 , HOH B:185 , HOH B:215 , HOH B:216 , HOH B:227 , HOH B:229	BINDING SITE FOR RESIDUE SO4 B 3

Asymmetric/Biological Unit

No.	Residues
1	A:80	-	A:83
2	B:80	-	B:83

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	YR596_MIMIV	33-139	2	A:33-139 B:33-139

(no "Exon" information available for 3GWN)

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:113
 aligned with YR596_MIMIV | Q5UP54 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:113
                                    41        51        61        71        81        91       101       111       121       131       141   
          YR596_MIMIV    32 HNGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRA 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ERV_ALR  PDB: A:33-139 UniProt: 33-139                                                                     ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3gwn A  32 ANGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRA 144
                                    41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with YR596_MIMIV | Q5UP54 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:113
                                    41        51        61        71        81        91       101       111       121       131       141   
          YR596_MIMIV    32 HNGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRA 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ERV_ALR  PDB: B:33-139 UniProt: 33-139                                                                     ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3gwn B  32 ANGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCRLCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLSYEDVVNKYESFRA 144
                                    41        51        61        71        81        91       101       111       121       131       141

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 '\|'

(no "SCOP Domain" information available for 3GWN)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3gwn)

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	3gwn
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UniProtKB/Swiss-Prot
	YR596_MIMIV \| Q5UP54	:	3td7

1jr8	ERV2P, A YEAST HOMOLOG
1oqc	ALR, A MAMMALIAN HOMOLG
2hj3	ATERV1, A PLANT HOMOLOG
3gwl	PB119L, A HOMOLOG FROM AFRICAN SWINE FEVER VIRUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (4, 4)

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