2I3Y - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 5

Authors :   K. L. Kavanagh, C. Johansson, A. Rojkova, C. Umeano, G. Bunkoczi, O. Gil F. Von Delft, J. Weigelt, C. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   21 Aug 06 (Deposition) - 12 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Thioredoxin Fold, Epididymal Androgen Related Protein, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Kavanagh, U. Oppermann
Crystal Structure Of Human Glutathione Peroxidase 5
To Be Published
PubMed: search

Molecule 1 - EPIDIDYMAL SECRETORY GLUTATHIONE PEROXIDASE
	Chains	:	A
	EC Number	:	1.11.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PNIC-BSA4 (PET DERIVATIVE)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GPX5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EPIDIDYMIS-SPECIFIC GLUTATHIONE PEROXIDASE-LIKE PROTEIN, EGLP, GLUTATHIONE PEROXIDASE 5

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:180 , HIS A:200 , HOH A:313	BINDING SITE FOR RESIDUE EDO A 221

(no "SS Bond" information available for 2I3Y)

Asymmetric Unit

No.	Residues
1	Arg A:123	-	Pro A:124
2	Asp A:172	-	Pro A:173

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061206	L	85	P	GPX5_HUMAN	Polymorphism	58554303	A	L	85	P
2	UniProt	VAR_012040	L	85	V	GPX5_HUMAN	Polymorphism	769188	A	L	85	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061206	L	85	P	GPX5_HUMAN	Polymorphism	58554303	A	L	85	P
2	UniProt	VAR_012040	L	85	V	GPX5_HUMAN	Polymorphism	769188	A	L	85	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_1	PS00460	Glutathione peroxidases active site.	GPX5_HUMAN	61-76	1	A:61-76
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX5_HUMAN	97-104	1	A:97-104

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTATHIONE_PEROXID_1	PS00460	Glutathione peroxidases active site.	GPX5_HUMAN	61-76	4	A:61-76
2	GLUTATHIONE_PEROXID_2	PS00763	Glutathione peroxidases signature 2.	GPX5_HUMAN	97-104	4	A:97-104

(no "Exon" information available for 2I3Y)

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:188
 aligned with GPX5_HUMAN | O75715 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:188
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           GPX5_HUMAN    31 DCHKDEKGTIYDYEAIALNKNEYVSFKQYVGKHILFVNVATYCGLTAQYPELNALQEELKPYGLVVLGFPCNQFGKQEPGDNKEILPGLKYVRPGGGFVPSFQLFEKGDVNGEKEQKVFSFLKHSCPHPSEILGTFKSISWDPVKVHDIRWNFEKFLVGPDGIPVMRWSHRATVSSVKTDILAYLKQF 218
               SCOP domains d2i3ya_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains ------2i3yA01 A:37-218 Glutaredoxin                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhh.eee......eee.hhhh..eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..........ee...........hhhhhhhhhhh............................eeee.....eeeee....hhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------P------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------GLUTATHIONE_PERO--------------------GLUTATHI------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i3y A  31 DCHKDEKGTIYDYEAIALNKNEYVSFKQYVGKHILFVNVATYCGLTAQYPELNALQEELKPYGLVVLGFPCNQFGKQEPGDNKEILPGLKYVRPGGGFVPSFQLFEKGDVNGEKEQKVFSFLKHSCPHPSEILGTFKSISWDPVKVHDIRWNFEKFLVGPDGIPVMRWSHRATVSSVKTDILAYLKQF 218
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Human (Homo sapiens) [TaxId: 9606] (87)

d2i3ya_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Human (Homo sapiens) (186)

2i3yA01

A:37-218

(no "Pfam Domain" information available for 2I3Y)

Asymmetric Unit(hide GO term definitions)

Chain A (GPX5_HUMAN | O75715)

molecular function
	GO:0004602	glutathione peroxidase activity	Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
	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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0000302	response to reactive oxygen species	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0097524	sperm plasma membrane	A plasma membrane that is part of a sperm cell.

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		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:123 - Pro A:124	[ RasMol ]
		Asp A:172 - Pro A:173	[ RasMol ]

Biological Unit
	Complete Structure
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