1V3U - JenaLib

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Title :   CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE IN APO FORM

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 :   05 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 (1, 7)

No.	Name	Count	Type	Full Name
1	CL	7	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:324 , ALA A:325 , HOH A:1045	BINDING SITE FOR RESIDUE CL A 1001
2	AC2	SOFTWARE	ALA B:149 , ALA B:151 , ALA B:173 , GLY B:174 , LYS B:178 , HOH B:1106 , HOH B:1119	BINDING SITE FOR RESIDUE CL B 1002
3	AC3	SOFTWARE	HIS B:12 , PHE B:13 , SER B:54 , LYS B:55 , HOH B:1126	BINDING SITE FOR RESIDUE CL B 1003
4	AC4	SOFTWARE	ARG A:70 , VAL A:72	BINDING SITE FOR RESIDUE CL A 1004
5	AC5	SOFTWARE	ASN B:321 , LYS B:324 , ALA B:325 , HOH B:1027	BINDING SITE FOR RESIDUE CL B 1005
6	AC6	SOFTWARE	ALA A:149 , ALA A:151 , ALA A:173 , LYS A:178 , HOH A:1257	BINDING SITE FOR RESIDUE CL A 1006
7	AC7	SOFTWARE	HIS B:12 , GLU B:59	BINDING SITE FOR RESIDUE CL B 1007

Asymmetric/Biological Unit

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

(no "Cis Peptide Bond" information available for 1V3U)

(no "SAP(SNP)/Variant" information available for 1V3U)

(no "PROSITE Motif" information available for 1V3U)

(no "Exon" information available for 1V3U)

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:316
 aligned with PTGR1_CAVPO | Q9EQZ5 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:330
                             1                                                                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
          PTGR1_CAVPO     - -MVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
               SCOP domains -d1v3ua1 A:1     -112,A:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase           d1v3ua2 A:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d1v3ua1 A:1-112,A:295-329           SCOP domains
               CATH domains 1v3uA01 A:-1     -120,A:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                    1v3uA02 A:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             1v3uA01 A:-1-120,A:299-329      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee..-----.hhh.eeeeeee........eeeeeeeee..hhhhhhh............eeeeeeee.........eeee......eeee....eee..--.....hhhhhhh..hhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee.....-------.....hhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v3u A  -1 FMVKAKSWTLKK-----PTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLL--WPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAIS-------LPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
                            ||       9 |     |19        29        39        49        59        69        79        89        99      |109       119       129       139       149       159       169       179       189       199       209       219       229       239   |     - |     259       269       279       289       299       309       319       329
                            ||        11    17                                                                                      106  |                                                                                                                                   243     251                                                                              
                           -1|                                                                                                         109                                                                                                                                                                                                                            
                             1

Chain B from PDB  Type:PROTEIN  Length:332
 aligned with PTGR1_CAVPO | Q9EQZ5 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:332
                               1                                                                                                                                                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  
          PTGR1_CAVPO     - ---MVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
               SCOP domains ---d1v3ub1 B:1-112,B:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                d1v3ub2 B:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d1v3ub1 B:1-112,B:295-329           SCOP domains
               CATH domains 1v3uB01 B:-3-120,B:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                           1v3uB02 B:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             1v3uB01 B:-3-120,B:299-329      CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-1v3uB01 B:153-289                                                                                                             ---------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-1v3uB02 B:153-289                                                                                                             ---------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeeee........hhh.eeeeeee........eeeeeeeee...hhhhhhhhh.........eeeeeeee.........eeee......eeee....eeee........hhhhhhh..hhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee.................hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3u B  -3 PEFMVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  
                             -1|                                                                                                                                                                                                                                                                                                                                        
                               1

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	1v3uB02	B:121-298
1b	1v3uA02	A: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	1v3uB01	B:-3-120,B:299-329
2b	1v3uA01	A:-1-120,A: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-1v3uB01	B:153-289
1b	ADH_zinc_N-1v3uB02	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 1v3v 2dm6

1v3t	THE SAME PROTEIN COMPLEXED WITH NADP
1v3v	THE SAME PROTEIN COMPLEXED WITH NADP AND 15-OXO-PGE2 RELATED ID: MY_001000011.2 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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