2ZAT - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A MAMMALIAN REDUCTASE

Authors :   N. Tanaka, K. Aoki, K. T. Nakamura

Date :   10 Oct 07 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,D  (1x)
Biol. Unit 3: B,C  (1x)
Biol. Unit 4: C,D  (1x)
Biol. Unit 5: A,B  (1x)

Keywords :   Alpha/Beta, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tanaka, K. Aoki, S. Ishikura, M. Nagano, Y. Imamura, A. Hara, K. T. Nakamura
Molecular Basis For Peroxisomal Localization Of Tetrameric Carbonyl Reductase.
Structure V. 16 388 2008
PubMed-ID: 18334214 | Reference-DOI: 10.1016/J.STR.2007.12.022
(for further references see the PDB file header)

Molecule 1 - DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 4
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.184
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCR T7/CT TOPO
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	NADPH-DEPENDENT CARBONYL REDUCTASE/NADP-RETINOL DEHYDROGENASE, CR, PHCR, PEROXISOMAL SHORT-CHAIN ALCOHOL DEHYDROGENASE, NADPH-DEPENDENT RETINOL DEHYDROGENASE/REDUCTASE, NDRD

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A			D
Biological Unit 3 (1x)	:		B	C
Biological Unit 4 (1x)	:			C	D
Biological Unit 5 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 2)

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

Biological Unit 4 (1, 2)

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

Biological Unit 5 (1, 2)

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

(no "Site" information available for 2ZAT)

(no "SS Bond" information available for 2ZAT)

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	4	A:151-179 B:151-179 C:151-179 D:151-179

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	4	A:151-179 B:151-179 C:151-179 D:151-179

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	2	A:151-179 - - D:151-179

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	2	- B:151-179 C:151-179 -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	2	- - C:151-179 D:151-179

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHRS4_PIG	170-198	2	A:151-179 B:151-179 - -

(no "Exon" information available for 2ZAT)

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:251
 aligned with DHRS4_PIG | Q8WNV7 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:251
                                    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 
            DHRS4_PIG    29 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 279
               SCOP domains d2zata_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2zatA00 A:10-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:151-179    --------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zat A  10 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 260
                                    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

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with DHRS4_PIG | Q8WNV7 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:251
                                    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 
            DHRS4_PIG    29 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 279
               SCOP domains d2zatb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2zatB00 B:10-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:151-179    --------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zat B  10 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 260
                                    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

Chain C from PDB  Type:PROTEIN  Length:251
 aligned with DHRS4_PIG | Q8WNV7 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:251
                                    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 
            DHRS4_PIG    29 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 279
               SCOP domains d2zatc_ C: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2zatC00 C:10-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:151-179    --------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zat C  10 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 260
                                    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

Chain D from PDB  Type:PROTEIN  Length:251
 aligned with DHRS4_PIG | Q8WNV7 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:251
                                    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 
            DHRS4_PIG    29 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 279
               SCOP domains d2zatd_ D: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2zatD00 D:10-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
           Pfam domains (1) ----------adh_short_C2-2zatD01 D:20-241                                                                                                                                                                                                 ------------------- Pfam domains (1)
           Pfam domains (2) ----------adh_short_C2-2zatD02 D:20-241                                                                                                                                                                                                 ------------------- Pfam domains (2)
           Pfam domains (3) ----------adh_short_C2-2zatD03 D:20-241                                                                                                                                                                                                 ------------------- Pfam domains (3)
           Pfam domains (4) ----------adh_short_C2-2zatD04 D:20-241                                                                                                                                                                                                 ------------------- Pfam domains (4)
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:151-179    --------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zat D  10 KPLENKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQENVDRTVATLQGEGLSVTGTVCHVGKAEDRERLVAMAVNLHGGVDILVSNAAVNPFFGNIIDATEEVWDKILHVNVKATVLMTKAVVPEMEKRGGGSVLIVSSVGAYHPFPNLGPYNVSKTALLGLTKNLAVELAPRNIRVNCLAPGLIKTNFSQVLWMDKARKEYMKESLRIRRLGNPEDCAGIVSFLCSEDASYITGETVVVGGGTASRL 260
                                    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

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Pig (Sus scrofa) [TaxId: 9823] (1)

1a	d2zata_	A:
1b	d2zatb_	B:
1c	d2zatc_	C:
1d	d2zatd_	D:

Asymmetric 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)

Pig (Sus scrofa) (21)

1a	2zatA00	A:10-260
1b	2zatB00	B:10-260
1c	2zatC00	C:10-260
1d	2zatD00	D:10-260

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short_C2 (98)

Sus scrofa (Pig) (1)

1a	adh_short_C2-2zatD01	D:20-241
1b	adh_short_C2-2zatD02	D:20-241
1c	adh_short_C2-2zatD03	D:20-241
1d	adh_short_C2-2zatD04	D:20-241

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DHRS4_PIG | Q8WNV7)

molecular function
	GO:0000253	3-keto sterol reductase activity	Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H(+).
	GO:0004090	carbonyl reductase (NADPH) activity	Catalysis of the reaction: R-CHOH-R' + NADP+ = R-CO-R' + 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:0001758	retinal dehydrogenase activity	Catalysis of the reaction: retinal + NAD+ + H2O = retinoate + NADH. Acts on both 11-trans and 13-cis forms of retinal.
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:0042574	retinal metabolic process	The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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