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Title :   CRYSTAL STRUCTURE OF LINOLEIC ACID BOUND IN THE CYCLOOXYGENASE CHANNEL OF PROSTAGLANDIN ENDOPEROXIDE H SYNTHASE-1.

Authors :   M. G. Malkowski, E. D. Thuresson, W. L. Smith, R. M. Garavito

Date :   18 Apr 01 (Deposition) - 12 Dec 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Membrane Protein, Fatty Acid, Linoleic Acid, Oxidoreductase, Peroxidase, Dioxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Malkowski, E. D. Thuresson, K. M. Lakkides, C. J. Rieke, R. Micielli, W. L. Smith, R. M. Garavito
Structure Of Eicosapentaenoic And Linoleic Acids In The Cyclooxygenase Site Of Prostaglandin Endoperoxide H Synthase-1.
J. Biol. Chem. V. 276 37547 2001
PubMed-ID: 11477109 | Reference-DOI: 10.1074/JBC.M105982200
(for further references see the PDB file header)

Molecule 1 - PROSTAGLANDIN ENDOPEROXIDE H SYNTHASE-1
	Chains	:	A
	EC Number	:	1.14.99.1
	Organ	:	SEMINAL VESSICLE
	Organism Common	:	SHEEP
	Organism Scientific	:	OVIS ARIES
	Organism Taxid	:	9940
	Synonym	:	CYCLOOXYGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (8, 14)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
4	COH	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING CO
5	EIC	1	Ligand/Ion	LINOLEIC ACID
6	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (8, 28)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	BMA	4	Ligand/Ion	BETA-D-MANNOSE
3	BOG	4	Ligand/Ion	B-OCTYLGLUCOSIDE
4	COH	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING CO
5	EIC	2	Ligand/Ion	LINOLEIC ACID
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:40 , TYR A:55 , ASN A:68 , NDG A:662	BINDING SITE FOR RESIDUE NAG A 661
02	AC2	SOFTWARE	TYR A:38 , ASP A:584 , NAG A:661	BINDING SITE FOR RESIDUE NDG A 662
03	AC3	SOFTWARE	GLU A:140 , ASN A:144 , TYR A:147 , LEU A:238 , NAG A:672	BINDING SITE FOR RESIDUE NAG A 671
04	AC4	SOFTWARE	MET A:216 , LEU A:238 , GLU A:239 , TYR A:242 , NAG A:671 , BMA A:673 , HOH A:814	BINDING SITE FOR RESIDUE NAG A 672
05	AC5	SOFTWARE	NAG A:672 , BMA A:674 , HOH A:824	BINDING SITE FOR RESIDUE BMA A 673
06	AC6	SOFTWARE	GLN A:243 , BMA A:673 , MAN A:675 , HOH A:824	BINDING SITE FOR RESIDUE BMA A 674
07	AC7	SOFTWARE	GLN A:243 , PRO A:270 , BMA A:674	BINDING SITE FOR RESIDUE MAN A 675
08	AC8	SOFTWARE	GLY A:278 , PRO A:281 , GLN A:406 , ASN A:410 , MET A:413 , ASP A:416 , NAG A:682	BINDING SITE FOR RESIDUE NAG A 681
09	AC9	SOFTWARE	GLN A:406 , NAG A:681	BINDING SITE FOR RESIDUE NAG A 682
10	BC1	SOFTWARE	SER A:87 , PHE A:88 , PHE A:91	BINDING SITE FOR RESIDUE BGC A 750
11	BC2	SOFTWARE	PRO A:86 , ILE A:89 , LEU A:112 , LEU A:115 , VAL A:119 , ARG A:120 , GLU A:524 , BOG A:752 , HOH A:872	BINDING SITE FOR RESIDUE BOG A 751
12	BC3	SOFTWARE	LEU A:115 , ASN A:122 , LEU A:123 , BOG A:751	BINDING SITE FOR RESIDUE BOG A 752
13	BC4	SOFTWARE	TYR A:148 , GLN A:203 , PHE A:210 , LYS A:211 , THR A:212 , LEU A:295 , ASN A:382 , TYR A:385 , HIS A:386 , TRP A:387 , HIS A:388 , MET A:391 , ILE A:444 , HIS A:446 , VAL A:447 , ASP A:450	BINDING SITE FOR RESIDUE COH A 601
14	BC5	SOFTWARE	VAL A:116 , ARG A:120 , PHE A:205 , PHE A:209 , TYR A:348 , VAL A:349 , LEU A:352 , TYR A:355 , PHE A:381 , TYR A:385 , TRP A:387 , ILE A:523 , ALA A:527 , SER A:530 , LEU A:534	BINDING SITE FOR RESIDUE EIC A 700

Asymmetric Unit

No.	Residues
1	A:36	-	A:47
2	A:37	-	A:159
3	A:41	-	A:57
4	A:59	-	A:69
5	A:569	-	A:575

Asymmetric Unit

No.	Residues
1	Ser A:126	-	Pro A:127

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PGH1_SHEEP_001 *	R	97	H	PGH1_SHEEP	---	---	A	R	97	H
2	UniProt	VAR_PGH1_SHEEP_002 *	D	164	G	PGH1_SHEEP	---	---	A	G	164	G
3	UniProt	VAR_PGH1_SHEEP_003 *	R	456	Q	PGH1_SHEEP	---	---	A	R	456	Q
4	UniProt	VAR_PGH1_SHEEP_004 *	E	520	K	PGH1_SHEEP	---	---	A	E	520	K
5	UniProt	VAR_PGH1_SHEEP_005 *	E	520	Q	PGH1_SHEEP	---	---	A	E	520	Q
6	UniProt	VAR_PGH1_SHEEP_006 *	M	525	I	PGH1_SHEEP	---	---	A	M	525	I
	* ID not provided by source

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

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PGH1_SHEEP_001 *	R	97	H	PGH1_SHEEP	---	---	A	R	97	H
2	UniProt	VAR_PGH1_SHEEP_002 *	D	164	G	PGH1_SHEEP	---	---	A	G	164	G
3	UniProt	VAR_PGH1_SHEEP_003 *	R	456	Q	PGH1_SHEEP	---	---	A	R	456	Q
4	UniProt	VAR_PGH1_SHEEP_004 *	E	520	K	PGH1_SHEEP	---	---	A	E	520	K
5	UniProt	VAR_PGH1_SHEEP_005 *	E	520	Q	PGH1_SHEEP	---	---	A	E	520	Q
6	UniProt	VAR_PGH1_SHEEP_006 *	M	525	I	PGH1_SHEEP	---	---	A	M	525	I
	* ID not provided by source

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_3	PS50026	EGF-like domain profile.	PGH1_SHEEP	32-70	1	A:32-70
2	PEROXIDASE_3	PS50292	Animal heme peroxidase superfamily profile.	PGH1_SHEEP	110-600	1	A:110-584

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_3	PS50026	EGF-like domain profile.	PGH1_SHEEP	32-70	2	A:32-70
2	PEROXIDASE_3	PS50292	Animal heme peroxidase superfamily profile.	PGH1_SHEEP	110-600	2	A:110-584

(no "Exon" information available for 1IGZ)

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:553
 aligned with PGH1_SHEEP | P05979 from UniProtKB/Swiss-Prot  Length:600

    Alignment length:553
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581   
           PGH1_SHEEP    32 PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMDTKGKKQLPDAEFLSRRFLLRRKFIPDPQSTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPD 584
               SCOP domains d1igza2 A:32-73                           d1igza1 A:74-584 Prostaglandin H2 synthase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1igzA01 A:33-73 Laminin                  1igzA02 A:74-583 Myeloperoxidase, subunit C                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.......eeeee...eeeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......ee......hhhhhhh....ee......................hhhhhhhhhh............hhhhhhhhhhhhh.............................hhhhhhhhh.........eee..eee................................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhh.............. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------H------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------------------------------------------------------------K----I----------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE EGF_3  PDB: A:32-70 UniProt: 32-70     ---------------------------------------PEROXIDASE_3  PDB: A:110-584 UniProt: 110-600                                                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1igz A  32 PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPD 584
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Myeloperoxidase, subunit C (39)

Homologous Superfamily: Myeloperoxidase, subunit C (39)

Sheep (Ovis aries) (18)

1igzA02

A:74-583

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Sheep (Ovis aries) (18)

1igzA01

A:33-73

(no "Pfam Domain" information available for 1IGZ)

Asymmetric Unit(hide GO term definitions)

Chain A (PGH1_SHEEP | P05979)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	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: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.
	GO:0004666	prostaglandin-endoperoxide synthase activity	Catalysis of the reaction: arachidonate + donor-H2 + 2 O2 = prostaglandin H2 + acceptor + 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:0019371	cyclooxygenase pathway	The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	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:0001516	prostaglandin biosynthetic process	The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
	GO:0006693	prostaglandin metabolic process	The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0031090	organelle membrane	A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:126 - Pro A:127	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1igz
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	PGH1_SHEEP \| P05979
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	1.14.99.1
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1diy	1DIY CONTAINS THE SAME PROTEIN COMPLEXED WITH ARACHIDONIC ACID (AA) IN THE CYCLOOXYGENASE CHANNEL.
1fe2	1FE2 CONTAINS THE SAME PROTEIN COMPLEXED WITH DIHOMO-GAMMA- LINOLENIC ACID (DHLA) IN THE CYCLOOXYGENASE CHANNEL.
1igx	1IGX CONTAINS THE SAME PROTEIN COMPLEXED WITH EICOSAPENTANOIC ACID (EPA) IN THE CYCLOOXYGENASE CHANNEL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 14)

Sites (14, 14)

SS Bonds (5, 5)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (25, 25)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File