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Title :   CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEXED WITH NADP AND 15-OXO-PGE2

Authors :   T. Hori, T. Yokomizo, H. Ago, M. Sugahara, G. Ueno, M. Yamamoto, T. Kumasaka, T. Shimizu, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   06 Nov 03 (Deposition) - 13 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Rossmann Fold, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hori, T. Yokomizo, H. Ago, M. Sugahara, G. Ueno, M. Yamamoto, T. Kumasaka, T. Shimizu, M. Miyano
Structural Basis Of Leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Catalytic Mechanism And A Possible Src Homology 3 Domain Binding Loop
J. Biol. Chem. V. 279 22615 2004
PubMed-ID: 15007077 | Reference-DOI: 10.1074/JBC.M312655200
(for further references see the PDB file header)

Molecule 1 - LEUKOTRIENE B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-KETO REDUCTASE
	Chains	:	A, B
	EC Number	:	1.3.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	DOMESTIC GUINEA PIG
	Organism Scientific	:	CAVIA PORCELLUS
	Organism Taxid	:	10141
	Synonym	:	LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO- PROSTAGLANDIN 13-REDUCTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	5OP	2	Ligand/Ion	(5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OICACID
2	CL	6	Ligand/Ion	CHLORIDE ION
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS B:12 , PHE B:13 , SER B:54 , LYS B:55	BINDING SITE FOR RESIDUE CL B 1001
02	AC2	SOFTWARE	GLU B:315 , ASN B:318 , HOH B:2533 , HOH B:2552 , HOH B:2556	BINDING SITE FOR RESIDUE CL B 1002
03	AC3	SOFTWARE	ASN A:318 , HOH A:1501	BINDING SITE FOR RESIDUE CL A 1003
04	AC4	SOFTWARE	HIS A:12 , PHE A:13 , SER A:54 , LYS A:55	BINDING SITE FOR RESIDUE CL A 1004
05	AC5	SOFTWARE	ARG A:51 , HOH A:1418 , HOH A:1760	BINDING SITE FOR RESIDUE CL A 1005
06	AC6	SOFTWARE	GLY B:15 , ARG B:51 , ASN B:246 , HOH B:2410	BINDING SITE FOR RESIDUE CL B 1006
07	AC7	SOFTWARE	PRO A:48 , MET A:124 , THR A:128 , GLY A:152 , ALA A:153 , VAL A:154 , GLY A:174 , LYS A:178 , TYR A:193 , ASN A:217 , VAL A:218 , CYS A:239 , GLY A:240 , ILE A:242 , SER A:243 , TYR A:245 , PHE A:270 , ILE A:271 , VAL A:272 , MET A:316 , LEU A:317 , GLY A:319 , ASN A:321 , 5OP A:1360 , HOH A:1361 , HOH A:1363 , HOH A:1364 , HOH A:1366 , HOH A:1369 , HOH A:1401 , HOH A:1406 , HOH A:1426 , HOH A:1626 , HOH A:1632 , HOH A:1687	BINDING SITE FOR RESIDUE NAP A 1350
08	AC8	SOFTWARE	PRO B:48 , MET B:124 , THR B:128 , GLY B:152 , ALA B:153 , VAL B:154 , ALA B:173 , GLY B:174 , LYS B:178 , TYR B:193 , ASN B:217 , VAL B:218 , CYS B:239 , GLY B:240 , ILE B:242 , SER B:243 , TYR B:245 , PHE B:270 , ILE B:271 , VAL B:272 , MET B:316 , LEU B:317 , GLY B:319 , ASN B:321 , 5OP B:2360 , HOH B:2366 , HOH B:2367 , HOH B:2368 , HOH B:2372 , HOH B:2379 , HOH B:2391 , HOH B:2475 , HOH B:2520 , HOH B:2522 , HOH B:2524 , HOH B:2603 , HOH B:2683	BINDING SITE FOR RESIDUE NAP B 2350
09	AC9	SOFTWARE	TYR A:49 , TYR A:245 , TYR A:273 , NAP A:1350 , HOH A:1379 , GLU B:258 , ILE B:261 , TYR B:262	BINDING SITE FOR RESIDUE 5OP A 1360
10	BC1	SOFTWARE	GLU A:258 , ILE A:261 , TYR A:262 , TYR B:49 , TYR B:245 , TYR B:273 , NAP B:2350 , HOH B:2395	BINDING SITE FOR RESIDUE 5OP B 2360

Asymmetric/Biological Unit

No.	Residues
1	A:137	-	A:213
2	B:137	-	B:213

(no "Cis Peptide Bond" information available for 1V3V)

(no "SAP(SNP)/Variant" information available for 1V3V)

(no "PROSITE Motif" information available for 1V3V)

(no "Exon" information available for 1V3V)

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:333
 aligned with PTGR1_CAVPO | Q9EQZ5 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:333
                                1                                                                                                                                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
          PTGR1_CAVPO     - ----MVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
               SCOP domains ----d1v3va1 A:1-112,A:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                d1v3va2 A:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d1v3va1 A:1-112,A:295-329           SCOP domains
               CATH domains 1v3vA01 A:-4-120,A:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                            1v3vA02 A:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             1v3vA01 A:-4-120,A:299-329      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........hhh.eeeeeee........eeeeeeeee..hhhhhhhhhh.........eeeeeeee.........eeee......eeee.....ee.........hhhhhhh..hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhh..eeeeeeeee..hhhhh..........hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3v A  -4 SPEFMVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
                               ||    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
                              -1|                                                                                                                                                                                                                                                                                                                                        
                                1

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with PTGR1_CAVPO | Q9EQZ5 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:328
                                    11        21        31        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        
          PTGR1_CAVPO     2 VKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
               SCOP domains d1v3vb1 B:2-112,B:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase               d1v3vb2 B:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d1v3vb1 B:2-112,B:295-329           SCOP domains
               CATH domains 1v3vB01 B:2-120,B:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                        1v3vB02 B:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             1v3vB01 B:2-120,B:299-329       CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-1v3vB01 B:153-289                                                                                                             ---------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-1v3vB02 B:153-289                                                                                                             ---------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee........hhh.eeeeeee........eeeeeeeee...hhhhhhhhh.........eeeeeeee.........eeee......eeee.....ee.........hhhhhhh..hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee..hhhhh..........hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3v B   2 VKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
                                    11        21        31        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

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Domestic guinea pig (Cavia porcellus) (5)

1a	1v3vA02	A:121-298
1b	1v3vB02	B:121-298

Architecture: Alpha-Beta Complex (3881)

Topology: Quinone Oxidoreductase; Chain A, domain 1 (131)

Homologous Superfamily: Medium-chain alcohol dehydrogenases, catalytic domain (131)

Domestic guinea pig (Cavia porcellus) (4)

2a	1v3vA01	A:-4-120,A:299-329
2b	1v3vB01	B:2-120,B:299-329

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: ADH_zinc_N (75)

Cavia porcellus (Guinea pig) (3)

1a	ADH_zinc_N-1v3vB01	B:153-289
1b	ADH_zinc_N-1v3vB02	B:153-289

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PTGR1_CAVPO | Q9EQZ5)

molecular function
	GO:0036132	13-prostaglandin reductase activity	Catalysis of the reaction: 15-keto-prostaglandin + NAD(P)H + H+ -> 13,14-dihydro-15-keto-prostaglandin + NAD(P)+. This reaction is the reduction of 15-keto-prostaglandin.
	GO:0047522	15-oxoprostaglandin 13-oxidase activity	Catalysis of the reaction: (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprostanoate + NAD(P)+ -> (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprosta-13-enoate + NAD(P)H + H+.
	GO:0032440	2-alkenal reductase [NAD(P)] activity	Catalysis of the reaction: n-alkanal + NAD(P)+ = alk-2-enal + NAD(P)H + H+.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	PTGR1_CAVPO \| Q9EQZ5	:	1v3t 1v3u 2dm6

1v3t	THE SAME PROTEIN COMPLEXED WITH NADP
1v3u	THE SAME PROTEIN IN APO FORM RELATED ID: MY_001000011.3 RELATED DB: TARGETDB

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

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SS Bonds (2, 2)

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