1IPF - JenaLib

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Title :   TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE

Authors :   A. Yamashita, M. Endo, T. Higashi, T. Nakatsu, Y. Yamada, J. Oda, H. Kato, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   09 May 01 (Deposition) - 03 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Oxidoreductase, Tropane Alkaloid Biosynthesis, Reduction Of Tropinone To Pseudotropine, Short-Chain Dehydrogenase, Tropinone, Laue Diffraction, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Yamashita, M. Endo, T. Higashi, T. Nakatsu, Y. Yamada, J. Oda, H. Kato
Capturing Enzyme Structure Prior To Reaction Initiation: Tropinone Reductase-Ii-Substrate Complexes
Biochemistry V. 42 5566 2003
PubMed-ID: 12741812 | Reference-DOI: 10.1021/BI0272712
(for further references see the PDB file header)

Molecule 1 - TROPINONE REDUCTASE-II
	Chains	:	A, B
	EC Number	:	1.1.1.236
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PETTR2
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET21D
	Expression System Vector Type	:	PLASMID
	Organ	:	CULTURED ROOT
	Organism Common	:	JIMSONWEED
	Organism Scientific	:	DATURA STRAMONIUM
	Organism Taxid	:	4076

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

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	TNE	2	Ligand/Ion	8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	TNE	2	Ligand/Ion	8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	TNE	4	Ligand/Ion	8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2	TNE	1	Ligand/Ion	8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:16 , SER A:18 , ARG A:19 , GLY A:20 , ILE A:21 , SER A:40 , ARG A:41 , CYS A:65 , ASP A:66 , LEU A:67 , ASN A:94 , ALA A:95 , ILE A:144 , SER A:145 , SER A:146 , TYR A:159 , LYS A:163 , GLY A:190 , VAL A:191 , ILE A:192 , THR A:194 , SER A:195 , LEU A:196 , VAL A:197 , TNE A:262 , HOH A:293	BINDING SITE FOR RESIDUE NDP A 261
2	AC2	SOFTWARE	TYR A:100 , SER A:146 , SER A:148 , GLU A:156 , TYR A:159 , GLY A:190 , LEU A:210 , LEU A:213 , NDP A:261	BINDING SITE FOR RESIDUE TNE A 262
3	AC3	SOFTWARE	GLY B:16 , SER B:18 , ARG B:19 , ILE B:21 , SER B:40 , ARG B:41 , GLU B:45 , CYS B:65 , ASP B:66 , LEU B:67 , ASN B:94 , GLY B:96 , ILE B:117 , ILE B:144 , SER B:145 , SER B:146 , TYR B:159 , LYS B:163 , PRO B:189 , GLY B:190 , VAL B:191 , ILE B:192 , THR B:194 , SER B:195 , LEU B:196 , VAL B:197 , TNE B:1262 , HOH B:1284	BINDING SITE FOR RESIDUE NDP B 1261
4	AC4	SOFTWARE	TYR B:100 , SER B:146 , GLU B:156 , TYR B:159 , VAL B:191 , VAL B:197 , NDP B:1261	BINDING SITE FOR RESIDUE TNE B 1262

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	TRN2_DATST	146-174	2	A:146-174 B:146-174

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	TRN2_DATST	146-174	2	A:146-174 B:146-174

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	TRN2_DATST	146-174	4	A:146-174 B:146-174

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.	TRN2_DATST	146-174	2	A:146-174 B:146-174

(no "Exon" information available for 1IPF)

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:259
 aligned with TRN2_DATST | P50163 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:259
                                    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         
           TRN2_DATST     2 AGRWNLEGCTALVTGGSRGIGYGIVEELASLGASVYTCSRNQKELNDCLTQWRSKGFKVEASVCDLSSRSERQELMNTVANHFHGKLNILVNNAGIVIYKEAKDYTVEDYSLIMSINFEAAYHLSVLAHPFLKASERGNVVFISSVSGALAVPYEAVYGATKGAMDQLTRCLAFEWAKDNIRVNGVGPGVIATSLVEMTIQDPEQKENLNKLIDRCALRRMGEPKELAAMVAFLCFPAASYVTGQIIYVDGGLMANCGF 260
               SCOP domains d1ipfa_ A: Tropinone reductase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ipfA00 A:2-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh......eeee.........hhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee..hhh.......hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.....hhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh.hhh......eeee...hhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:146-174    -------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipf A   2 AGRWNLEGCTALVTGGSRGIGYGIVEELASLGASVYTCSRNQKELNDCLTQWRSKGFKVEASVCDLSSRSERQELMNTVANHFHGKLNILVNNAGIVIYKEAKDYTVEDYSLIMSINFEAAYHLSVLAHPFLKASERGNVVFISSVSGALAVPYEAVYGATKGAMDQLTRCLAFEWAKDNIRVNGVGPGVIATSLVEMTIQDPEQKENLNKLIDRCALRRMGEPKELAAMVAFLCFPAASYVTGQIIYVDGGLMANCGF 260
                                    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

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with TRN2_DATST | P50163 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:259
                                    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         
           TRN2_DATST     2 AGRWNLEGCTALVTGGSRGIGYGIVEELASLGASVYTCSRNQKELNDCLTQWRSKGFKVEASVCDLSSRSERQELMNTVANHFHGKLNILVNNAGIVIYKEAKDYTVEDYSLIMSINFEAAYHLSVLAHPFLKASERGNVVFISSVSGALAVPYEAVYGATKGAMDQLTRCLAFEWAKDNIRVNGVGPGVIATSLVEMTIQDPEQKENLNKLIDRCALRRMGEPKELAAMVAFLCFPAASYVTGQIIYVDGGLMANCGF 260
               SCOP domains d1ipfb_ B: Tropinone reductase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ipfB00 B:2-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh......eeee.........hhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeee..hhh.......hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.....hhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh.hhh......eeee...hhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:146-174    -------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipf B   2 AGRWNLEGCTALVTGGSRGIGYGIVEELASLGASVYTCSRNQKELNDCLTQWRSKGFKVEASVCDLSSRSERQELMNTVANHFHGKLNILVNNAGIVIYKEAKDYTVEDYSLIMSINFEAAYHLSVLAHPFLKASERGNVVFISSVSGALAVPYEAVYGATKGAMDQLTRCLAFEWAKDNIRVNGVGPGVIATSLVEMTIQDPEQKENLNKLIDRCALRRMGEPKELAAMVAFLCFPAASYVTGQIIYVDGGLMANCGF 260
                                    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

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(

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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: Tyrosine-dependent oxidoreductases (503)

Protein domain: Tropinone reductase (6)

Jimsonweed (Datura stramonium), II [TaxId: 4076] (4)

1a	d1ipfa_	A:
1b	d1ipfb_	B:

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)

Jimsonweed (Datura stramonium) (5)

1a	1ipfA00	A:2-260
1b	1ipfB00	B:2-260

(no "Pfam Domain" information available for 1IPF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRN2_DATST | P50163)

molecular function
	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:0050358	tropinone reductase activity	Catalysis of the reaction: NADP(+) + pseudotropine = H(+) + NADPH + tropinone.
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:0009710	tropane alkaloid biosynthetic process	The chemical reactions and pathways resulting in the breakdown of tropane alkaloids, compounds containing the 8-methyl-8-azabicyclo(3.2.1)octane ring system.

Asymmetric Unit
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	TRN2_DATST \| P50163	:	1ipe 2ae1 2ae2

1ipe	1IPE CONTAINS THE SAME PROTEIN COMPLEXED WITH NADPH RELATED ID: MY_001000042.2 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (2, 4)

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