3COT - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN LIVER DELTA(4)-3-KETOSTEROID 5BETA-REDUCTASE (AKR1D1) IN COMPLEX WITH PROGESTERONE AND NADP. RESOLUTION: 2.03 A.

Authors :   L. Di Costanzo, J. Drury, T. M. Penning, D. W. Christianson

Date :   29 Mar 08 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Steroid C-C Double Bond Reduction, 5Beta Reductase, E120, Bile Acid Catabolism, Cytoplasm, Disease Mutation, Lipid Metabolism, Nadp, Oxidoreductase, Steroid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Di Costanzo, J. E. Drury, T. M. Penning, D. W. Christianson
Crystal Structure Of Human Liver {Delta}4-3-Ketosteroid 5{Beta}-Reductase (Akr1D1) And Implications For Substrate Binding And Catalysis.
J. Biol. Chem. V. 283 16830 2008
PubMed-ID: 18407998 | Reference-DOI: 10.1074/JBC.M801778200
(for further references see the PDB file header)

Molecule 1 - 3-OXO-5-BETA-STEROID 4-DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28(A)
	Expression System Vector Type	:	PLASMID
	Gene	:	AKR1D1, SRD5B1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DELTA(4)-3-KETOSTEROID 5-BETA-REDUCTASE, ALDO- KETO REDUCTASE FAMILY 1 MEMBER D1

		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	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	STR	2	Ligand/Ion	PROGESTERONE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	STR	1	Ligand/Ion	PROGESTERONE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	STR	1	Ligand/Ion	PROGESTERONE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:24 , THR B:25 , TYR B:26 , ASP B:53 , TYR B:58 , LYS B:87 , SER B:169 , ASN B:170 , GLN B:193 , TYR B:219 , SER B:220 , PRO B:221 , LEU B:222 , GLY B:223 , THR B:224 , SER B:225 , LEU B:239 , ALA B:256 , ILE B:271 , PRO B:272 , LYS B:273 , SER B:274 , PHE B:275 , ARG B:279 , GLU B:282 , ASN B:283	BINDING SITE FOR RESIDUE NAP B 3901
2	AC2	SOFTWARE	GLY A:24 , THR A:25 , TYR A:26 , ASP A:53 , TYR A:58 , LYS A:87 , SER A:169 , ASN A:170 , GLN A:193 , TYR A:219 , SER A:220 , PRO A:221 , LEU A:222 , GLY A:223 , THR A:224 , SER A:225 , LEU A:239 , ALA A:256 , ILE A:271 , PRO A:272 , LYS A:273 , SER A:274 , PHE A:275 , ARG A:279 , GLU A:282 , ASN A:283	BINDING SITE FOR RESIDUE NAP A 3902
3	AC3	SOFTWARE	TYR B:26 , TYR B:58 , GLU B:120 , TRP B:230 , TRP B:314	BINDING SITE FOR RESIDUE STR B 1500
4	AC4	SOFTWARE	TYR A:26 , TYR A:58 , GLU A:120 , TYR A:132 , TRP A:230	BINDING SITE FOR RESIDUE STR A 1501

(no "SS Bond" information available for 3COT)

(no "Cis Peptide Bond" information available for 3COT)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033007	L	106	F	AK1D1_HUMAN	Disease (CBAS2)	121918343	A/B	L	106	F
2	UniProt	VAR_044430	P	133	R	AK1D1_HUMAN	Disease (CBAS2)	267606649	A/B	P	133	R
3	UniProt	VAR_033008	P	198	L	AK1D1_HUMAN	Disease (CBAS2)	121918342	A/B	P	198	L
4	UniProt	VAR_044431	R	261	C	AK1D1_HUMAN	Disease (CBAS2)	267606650	A/B	R	261	C

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

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033007	L	106	F	AK1D1_HUMAN	Disease (CBAS2)	121918343	A	L	106	F
2	UniProt	VAR_044430	P	133	R	AK1D1_HUMAN	Disease (CBAS2)	267606649	A	P	133	R
3	UniProt	VAR_033008	P	198	L	AK1D1_HUMAN	Disease (CBAS2)	121918342	A	P	198	L
4	UniProt	VAR_044431	R	261	C	AK1D1_HUMAN	Disease (CBAS2)	267606650	A	R	261	C

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033007	L	106	F	AK1D1_HUMAN	Disease (CBAS2)	121918343	B	L	106	F
2	UniProt	VAR_044430	P	133	R	AK1D1_HUMAN	Disease (CBAS2)	267606649	B	P	133	R
3	UniProt	VAR_033008	P	198	L	AK1D1_HUMAN	Disease (CBAS2)	121918342	B	P	198	L
4	UniProt	VAR_044431	R	261	C	AK1D1_HUMAN	Disease (CBAS2)	267606650	B	R	261	C

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

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.	AK1D1_HUMAN	48-65	2	A:48-65 B:48-65
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1D1_HUMAN	154-171	2	A:154-171 B:154-171
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	AK1D1_HUMAN	271-286	2	A:271-286 B:271-286

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.	AK1D1_HUMAN	48-65	1	A:48-65 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1D1_HUMAN	154-171	1	A:154-171 -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	AK1D1_HUMAN	271-286	1	A:271-286 -

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.	AK1D1_HUMAN	48-65	1	- B:48-65
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1D1_HUMAN	154-171	1	- B:154-171
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	AK1D1_HUMAN	271-286	1	- B:271-286

(no "Exon" information available for 3COT)

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:325
 aligned with AK1D1_HUMAN | P51857 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:325
                                    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     
          AK1D1_HUMAN     2 DLSAASHRIPLSDGNSIPIIGLGTYSEPKSTPKGACATSVKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPEMVRPTLERTLRVLQLDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRRQLELILNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPIWVNVSSPPLLKDALLNSLGKRYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTEEEMKDIEALNKNVRFVELLMWRDHPEYPFHDEY 326
               SCOP domains d3cota_ A: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3cotA00 A:2-326 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eee...ee..........hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee....ee................ee..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------F--------------------------R----------------------------------------------------------------L--------------------------------------------------------------C----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cot A   2 DLSAASHRIPLSDGNSIPIIGLGTYSEPKSTPKGACATSVKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPEMVRPTLERTLRVLQLDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRRQLELILNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPIWVNVSSPPLLKDALLNSLGKRYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTEEEMKDIEALNKNVRFVELLMWRDHPEYPFHDEY 326
                                    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:325
 aligned with AK1D1_HUMAN | P51857 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:325
                                    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     
          AK1D1_HUMAN     2 DLSAASHRIPLSDGNSIPIIGLGTYSEPKSTPKGACATSVKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPEMVRPTLERTLRVLQLDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRRQLELILNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPIWVNVSSPPLLKDALLNSLGKRYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTEEEMKDIEALNKNVRFVELLMWRDHPEYPFHDEY 326
               SCOP domains d3cotb_ B: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3cotB00 B:2-326 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eee...ee...hhhhh..hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhh....hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------F--------------------------R----------------------------------------------------------------L--------------------------------------------------------------C----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cot B   2 DLSAASHRIPLSDGNSIPIIGLGTYSEPKSTPKGACATSVKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPEMVRPTLERTLRVLQLDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRRQLELILNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPIWVNVSSPPLLKDALLNSLGKRYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTEEEMKDIEALNKNVRFVELLMWRDHPEYPFHDEY 326
                                    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(

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Folds(

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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: automated matches (62)

Human (Homo sapiens) [TaxId: 9606] (48)

1a	d3cota_	A:
1b	d3cotb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

Human (Homo sapiens) (116)

1a	3cotA00	A:2-326
1b	3cotB00	B:2-326

(no "Pfam Domain" information available for 3COT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AK1D1_HUMAN | P51857)

molecular function
	GO:0004033	aldo-keto reductase (NADP) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
	GO:0047787	delta4-3-oxosteroid 5beta-reductase activity	Catalysis of the reactions: (1) 5beta-cholestan-3-one + NADP+ = cholest-4-en-3-one + NADPH + H+ and (2) 17,21-dihydroxy-5beta-pregnane-3,11,20-trione + NADP+ = cortisone + NADPH + 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:0005496	steroid binding	Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
biological process
	GO:0008207	C21-steroid hormone metabolic process	The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.
	GO:0008209	androgen metabolic process	The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
	GO:0006699	bile acid biosynthetic process	The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.
	GO:0030573	bile acid catabolic process	The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile.
	GO:0006707	cholesterol catabolic process	The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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	3cot
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	AK1D1_HUMAN \| P51857	:	3bur 3buv 3bv7 3caq 3cas 3cav 3cmf 3dop 3g1r 3uzw 3uzx 3uzy 3uzz

3cmf	THE SAME PROTEIN IN COMPLEX WITH CORTISOEN AND NADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (3, 6)

Exons (0, 0)

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Related Entries Specified in the PDB File