1Q5M - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   BINARY COMPLEX OF RABBIT 20ALPHA-HYDROXYSTEROID DEHYDROGENASE WITH NADPH

Authors :   J. F. Couture, P. Legrand, L. Cantin, F. Labrie, V. Luu-The, R. Breton

Date :   08 Aug 03 (Deposition) - 18 May 04 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.32

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

Keywords :   Nadph, Hsd, Hydroxysteroid Dehydrogenase, Aldo-Keto Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Couture, P. Legrand, L. Cantin, F. Labrie, V. Luu-The, R. Breton
Loop Relaxation, A Mechanism That Explains The Reduced Specificity Of Rabbit 20Alpha-Hydroxysteroid Dehydrogenase, A Member Of The Aldo-Keto Reductase Superfamily.
J. Mol. Biol. V. 339 89 2004
PubMed-ID: 15123423 | Reference-DOI: 10.1016/J.JMB.2004.03.035

Molecule 1 - PROSTAGLANDIN-E2 9-REDUCTASE
	Chains	:	A, B
	EC Number	:	1.1.1.189, 1.1.1.149
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21DE3(PLYSS)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	20-ALPHA-HYDROXYSTEROID DEHYDROGENASE, 20-ALPHA-HSD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:11 , ASP A:12 , TYR A:184 , LYS A:185 , HOH A:1026 , HOH A:1256	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	SER B:11 , ASP B:12 , TYR B:184 , LYS B:185 , HOH B:1111 , HOH B:1312 , HOH B:1401	BINDING SITE FOR RESIDUE SO4 B 1002
3	AC3	SOFTWARE	GLY A:22 , THR A:23 , TYR A:24 , ASP A:50 , TYR A:55 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , TYR A:216 , SER A:217 , ALA A:218 , LEU A:219 , GLY A:220 , SER A:221 , HIS A:222 , LEU A:236 , ALA A:253 , LEU A:268 , LYS A:270 , SER A:271 , PHE A:272 , THR A:273 , ARG A:276 , GLU A:279 , ASN A:280 , HOH A:1009 , HOH A:1029 , HOH A:1061 , HOH A:1064 , HOH A:1230 , HOH A:1279 , HOH A:1280 , HOH A:1300 , HOH A:1310	BINDING SITE FOR RESIDUE NDP A 1003
4	AC4	SOFTWARE	GLY B:22 , THR B:23 , TYR B:24 , ASP B:50 , TYR B:55 , LYS B:84 , HIS B:117 , SER B:166 , ASN B:167 , GLN B:190 , TYR B:216 , SER B:217 , ALA B:218 , LEU B:219 , GLY B:220 , SER B:221 , HIS B:222 , ALA B:253 , LEU B:268 , LYS B:270 , SER B:271 , PHE B:272 , THR B:273 , ARG B:276 , GLU B:279 , ASN B:280 , HOH B:1010 , HOH B:1029 , HOH B:1118 , HOH B:1130 , HOH B:1167 , HOH B:1292 , HOH B:1310 , HOH B:1322 , HOH B:1323 , HOH B:1332 , HOH B:1360	BINDING SITE FOR RESIDUE NDP B 1004

(no "SS Bond" information available for 1Q5M)

(no "Cis Peptide Bond" information available for 1Q5M)

(no "SAP(SNP)/Variant" information available for 1Q5M)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PE2R_RABIT	45-62	2	A:45-62 B:45-62
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PE2R_RABIT	151-168	2	A:151-168 B:151-168
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	PE2R_RABIT	268-283	2	A:268-283 B:268-283

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PE2R_RABIT	45-62	1	A:45-62 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PE2R_RABIT	151-168	1	A:151-168 -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	PE2R_RABIT	268-283	1	A:268-283 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PE2R_RABIT	45-62	1	- B:45-62
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PE2R_RABIT	151-168	1	- B:151-168
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	PE2R_RABIT	268-283	1	- B:268-283

(no "Exon" information available for 1Q5M)

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:322
 aligned with PE2R_RABIT | P80508 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:322
                                    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  
           PE2R_RABIT     2 DPKFQRVALSDGHFIPVLGFGTYAPEEVPKSKAMEATKIAIDAGFRHIDSAYFYKNEKEVGLAIRSKIADGTVKREDIFYTSKLWCTFHRPELVRPSLEDSLKNLQLDYVDLYIIHFPTALKPGVEIIPTDEHGKAIFDTVDICATWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYLNQGKLLEFCKSKGIVLVAYSALGSHREPEWVDQSAPVLLEDPLIGALAKKHQQTPALIALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYVTADFAIGHPNYPFSDEY 323
               SCOP domains d1q5ma_ A: 20alpha-hydroxysteroid dehydrogenase                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1q5mA00 A:2-323 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eee.....eee.eeee.......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5m A   2 DPKFQRVALSDGHFIPVLGFGTYAPEEVPKSKAMEATKIAIDAGFRHIDSAYFYKNEKEVGLAIRSKIADGTVKREDIFYTSKLWCTFHRPELVRPSLEDSLKNLQLDYVDLYIIHFPTALKPGVEIIPTDEHGKAIFDTVDICATWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYLNQGKLLEFCKSKGIVLVAYSALGSHREPEWVDQSAPVLLEDPLIGALAKKHQQTPALIALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYVTADFAIGHPNYPFSDEY 323
                                    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

Chain B from PDB  Type:PROTEIN  Length:322
 aligned with PE2R_RABIT | P80508 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:322
                                    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  
           PE2R_RABIT     2 DPKFQRVALSDGHFIPVLGFGTYAPEEVPKSKAMEATKIAIDAGFRHIDSAYFYKNEKEVGLAIRSKIADGTVKREDIFYTSKLWCTFHRPELVRPSLEDSLKNLQLDYVDLYIIHFPTALKPGVEIIPTDEHGKAIFDTVDICATWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYLNQGKLLEFCKSKGIVLVAYSALGSHREPEWVDQSAPVLLEDPLIGALAKKHQQTPALIALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYVTADFAIGHPNYPFSDEY 323
               SCOP domains d1q5mb_ B: 20alpha-hydroxysteroid dehydrogenase                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1q5mB00 B:2-323 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------------Aldo_ket_red-1q5mB01 B:18-301                                                                                                                                                                                                                                                               ---------------------- Pfam domains (1)
           Pfam domains (2) ----------------Aldo_ket_red-1q5mB02 B:18-301                                                                                                                                                                                                                                                               ---------------------- Pfam domains (2)
         Sec.struct. author hhhh.eee.....eee.eeee.......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5m B   2 DPKFQRVALSDGHFIPVLGFGTYAPEEVPKSKAMEATKIAIDAGFRHIDSAYFYKNEKEVGLAIRSKIADGTVKREDIFYTSKLWCTFHRPELVRPSLEDSLKNLQLDYVDLYIIHFPTALKPGVEIIPTDEHGKAIFDTVDICATWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYLNQGKLLEFCKSKGIVLVAYSALGSHREPEWVDQSAPVLLEDPLIGALAKKHQQTPALIALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYVTADFAIGHPNYPFSDEY 323
                                    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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: Aldo-keto reductases (NADP) (251)

Protein domain: 20alpha-hydroxysteroid dehydrogenase (3)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (2)

1a	d1q5ma_	A:
1b	d1q5mb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

Rabbit (Oryctolagus cuniculus) (2)

1a	1q5mA00	A:2-323
1b	1q5mB00	B:2-323

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Aldo_ket_red] (94)

Family: Aldo_ket_red (94)

Oryctolagus cuniculus (Rabbit) (2)

1a	Aldo_ket_red-1q5mB01	B:18-301
1b	Aldo_ket_red-1q5mB02	B:18-301

Asymmetric Unit(hide GO term definitions)

Chain A,B (PE2R_RABIT | P80508)

molecular function
	GO:0047006	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity	Catalysis of the reaction: NAD(P)+ + 17-alpha,20-alpha-dihydroxypregn-4-en-3-one = NAD(P)H + H+ + 17-alpha-hydroxyprogesterone.
	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:0050221	prostaglandin-E2 9-reductase activity	Catalysis of the reaction: (5Z,13E)-(15S)-9-alpha,11-alpha,15-trihydroxyprosta-5,13-dienoate + NADP+ = (5Z,13E)-(15S)-11-alpha,15-dihydroxy-9-oxoprosta-5,13-dienoate + NADPH.
biological process
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	1q5m
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	PE2R_RABIT \| P80508	:	1q13

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