2DM6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEX

Authors :   T. Hori, J. Ishijima, T. Yokomizo, H. Ago, T. Shimizu, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   20 Apr 06 (Deposition) - 28 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   T. Hori, J. Ishijima, T. Yokomizo, H. Ago, T. Shimizu, M. Miyano
Crystal Structure Of Anti-Configuration Of Indomethacin And Leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complex Reveals The Structural Basis Of Broad Spectrum Indomethacin Efficacy
J. Biochem. (Tokyo) V. 140 457 2006
PubMed-ID: 16916844 | Reference-DOI: 10.1093/JB/MVJ176
(for further references see the PDB file header)

Molecule 1 - NADP-DEPENDENT LEUKOTRIENE B4 12- HYDROXYDEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.1.74, 1.3.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	DOMESTIC GUINEA PIG
	Organism Scientific	:	CAVIA PORCELLUS
	Organism Taxid	:	10141
	Synonym	:	DEHYDROGENASE/REDUCTASE, LTB4, 12-HD, 15- OXOPROSTAGLANDIN 13-REDUCTASE, PGR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	IMN	1	Ligand/Ion	INDOMETHACIN
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:48 , MET A:124 , THR A:128 , GLY A:152 , ALA A:153 , VAL A:154 , ALA A:173 , GLY A:174 , LYS A:178 , TYR A:193 , ASN A:217 , VAL A:218 , CYS A:239 , GLY A:240 , ALA A:241 , 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 , HOH A:1403 , HOH A:1405 , HOH A:1412 , HOH A:1421 , HOH A:1422 , HOH A:1428 , HOH A:1443 , HOH A:1488 , HOH A:1574 , HOH A:1613 , HOH A:1619	BINDING SITE FOR RESIDUE NAP A 1400
2	AC2	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 , HOH B:5005 , HOH B:5006 , HOH B:5011 , HOH B:5034 , HOH B:5066 , HOH B:5079 , HOH B:5081 , HOH B:5083 , HOH B:5188 , HOH B:5195 , HOH B:5198 , HOH B:5291	BINDING SITE FOR RESIDUE NAP B 2400
3	AC3	SOFTWARE	TYR A:49 , ILE A:52 , ALA A:53 , ARG A:56 , TYR A:245 , ILE A:271 , HOH A:1566 , GLU B:258 , ILE B:261 , TYR B:262	BINDING SITE FOR RESIDUE IMN A 1401
4	AC4	SOFTWARE	GLU A:307 , LYS B:304 , GLU B:307 , ASN B:308 , HOH B:5252	BINDING SITE FOR RESIDUE TAM B 5000

Asymmetric/Biological Unit

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

(no "Cis Peptide Bond" information available for 2DM6)

(no "SAP(SNP)/Variant" information available for 2DM6)

(no "PROSITE Motif" information available for 2DM6)

(no "Exon" information available for 2DM6)

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:331
 aligned with PTGR1_CAVPO | Q9EQZ5 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:331
                              1                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
          PTGR1_CAVPO     - --MVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
               SCOP domains d2dm6a1 A:-2-112,A:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                 d2dm6a2 A:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d2dm6a1 A:-2-112,A:295-329          SCOP domains
               CATH domains 2dm6A01 A:-2-120,A:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                          2dm6A02 A:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             2dm6A01 A:-2-120,A:299-329      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee........hhh.eeeeeee........eeeeeeeee..hhhhhhh............eeeeeeee.........eeee......eeee....eee.........hhhhhhh..hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee..hhhhh..........hhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dm6 A  -2 EFMVKAKSWTLKKHFQGKPTQSDFELKTVELPPLKNGEVLLEALFLSVDPYMRIASKRLKEGAVMMGQQVARVVESKNSAFPAGSIVLAQSGWTTHFISDGKGLEKLLTEWPDKLPLSLALGTIGMPGLTAYFGLLEVCGVKGGETVLVSAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKIAYLKQIGFDAAFNYKTVNSLEEALKKASPDGYDCYFDNVGGEFLNTVLSQMKDFGKIAICGAISVYNRMDQLPPGPSPESIIYKQLRIEGFIVYRWQGDVREKALRDLMKWVLEGKIQYHEHVTKGFENMPAAFIEMLNGANLGKAVVTA 329
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
                             ||                                                                                                                                                                                                                                                                                                                                        
                            -1|                                                                                                                                                                                                                                                                                                                                        
                              1

Chain B 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 d2dm6b1 B:-4-112,B:295-329 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                   d2dm6b2 B:113-294 Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase                                                                                              d2dm6b1 B:-4-112,B:295-329          SCOP domains
               CATH domains 2dm6B01 B:-4-120,B:299-329 Medium-chain alcohol dehydrogenases, catalytic domain                                            2dm6B02 B:121-298 NAD(P)-binding Rossmann-like Domain                                                                                                                             2dm6B01 B:-4-120,B:299-329      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........hhh.eeeeeee........eeeeeeeee..hhhhhhhhhh.........eeeeeeee.........eeee......eeee....eee.........hhhhhhh..hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee..hhhhh..........hhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dm6 B  -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

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		→ 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	2dm6A02	A:121-298
1b	2dm6B02	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	2dm6B01	B:-4-120,B:299-329
2b	2dm6A01	A:-2-120,A:299-329

(no "Pfam Domain" information available for 2DM6)

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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	2dm6
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	1.3.1.48
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	1.3.1.74
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	PTGR1_CAVPO \| Q9EQZ5	:	1v3t 1v3u 1v3v

1v3t	THE SAME PROTEIN COMPLEXED WITH NADP+.
1v3u	THE SAME PROTEIN IN APO FORM. RELATED ID: MY_001000011.4 RELATED DB: TARGETDB
1v3v	THE SAME PROTEIN COMPLEXED WITH NADP+ AND 15-OXO-PGE2.

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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