1ICP - JenaLib

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Title :   CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH PEG400

Authors :   C. Breithaupt, J. Strassner, U. Breitinger, R. Huber, P. Macheroux, A. Schaller, T. Clausen

Date :   02 Apr 01 (Deposition) - 16 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Beta-Alpha-Barrel, Protein-Fmn-Peg Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Breithaupt, J. Strassner, U. Breitinger, R. Huber, P. Macheroux, A. Schaller, T. Clausen
X-Ray Structure Of 12-Oxophytodienoate Reductase 1 Provides Structural Insight Into Substrate Binding And Specificity Within The Family Of Oye.
Structure V. 9 419 2001
PubMed-ID: 11377202 | Reference-DOI: 10.1016/S0969-2126(01)00602-5
(for further references see the PDB file header)

Molecule 1 - 12-OXOPHYTODIENOATE REDUCTASE 1
	Chains	:	A, B
	EC Number	:	1.3.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-G
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	OPR1
	Mutation	:	YES
	Organism Scientific	:	SOLANUM LYCOPERSICUM
	Organism Taxid	:	4081
	Synonym	:	OPR1

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	2PE	2	Ligand/Ion	NONAETHYLENE GLYCOL
2	CL	1	Ligand/Ion	CHLORIDE ION
3	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:205 , SER A:206 , ARG B:156	BINDING SITE FOR RESIDUE CL A 505
2	AC2	SOFTWARE	ALA B:244 , HIS B:245 , TYR B:246 , ARG B:279	BINDING SITE FOR RESIDUE SO4 B 506
3	AC3	SOFTWARE	ALA A:244 , HIS A:245 , TYR A:246 , ARG A:279 , HOH A:739	BINDING SITE FOR RESIDUE SO4 A 507
4	AC4	SOFTWARE	ALA A:34 , PRO A:35 , LEU A:36 , THR A:37 , ALA A:68 , GLN A:110 , HIS A:187 , HIS A:190 , ARG A:239 , GLY A:308 , GLY A:309 , TYR A:329 , GLY A:330 , ARG A:331 , PHE A:357 , TYR A:358 , 2PE A:503 , HOH A:508 , HOH A:511 , HOH A:513 , HOH A:537	BINDING SITE FOR RESIDUE FMN A 501
5	AC5	SOFTWARE	ALA B:34 , PRO B:35 , LEU B:36 , THR B:37 , ALA B:68 , GLN B:110 , HIS B:187 , HIS B:190 , ARG B:239 , GLY B:308 , GLY B:309 , TYR B:329 , GLY B:330 , ARG B:331 , PHE B:357 , TYR B:358 , 2PE B:504 , HOH B:522 , HOH B:525 , HOH B:536 , HOH B:722	BINDING SITE FOR RESIDUE FMN B 502
6	AC6	SOFTWARE	THR A:37 , GLN A:39 , GLY A:77 , TYR A:78 , GLN A:140 , ALA A:149 , TYR A:192 , TYR A:246 , ARG A:279 , GLY A:309 , ARG A:331 , TYR A:358 , FMN A:501 , HOH A:620 , HOH A:712 , HOH A:755	BINDING SITE FOR RESIDUE 2PE A 503
7	AC7	SOFTWARE	THR B:37 , GLN B:39 , GLY B:77 , TYR B:78 , PHE B:122 , GLN B:140 , ILE B:141 , MET B:142 , ALA B:149 , TYR B:192 , ARG B:331 , TYR B:358 , FMN B:502 , HOH B:723 , HOH B:741	BINDING SITE FOR RESIDUE 2PE B 504

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

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

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

(no "PROSITE Motif" information available for 1ICP)

(no "Exon" information available for 1ICP)

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:358
 aligned with OPR1_SOLLC | Q9XG54 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:364
                                    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       269       279       289       299       309       319       329       339       349       359       369    
           OPR1_SOLLC    10 QVDKIPLMSPCKMGKFELCHRVVLAPLTRQRSYGYIPQPHAILHYSQRSTNGGLLIGEATVISETGIGYKDVPGIWTKEQVEAWKPIVDAVHAKGGIFFCQIWHVGRVSNKDFQPNGEDPISCTDRGLTPQIRSNGIDIAHFTRPRRLTTDEIPQIVNEFRVAARNAIEAGFDGVEIHGAHGYLIDQFMKDQVNDRSDKYGGSLENRCRFALEIVEAVANEIGSDRVGIRISPFAHYNEAGDTNPTALGLYMVESLNKYDLAYCHVVEPRMKTAWEKIECTESLVPMRKAYKGTFIVAGGYDREDGNRALIEDRADLVAYGRLFISNPDLPKRFELNAPLNKYNRDTFYTSDPIVGYTDYPFLE 373
               SCOP domains d1icpa_ A: 12-oxophytodienoate reductase (OPR, OYE homolog)                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1icpA00 A:10-373 Aldolase class I                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.eee..eee...eee.......hhhhh.hhhhhhhhhhh.....eee...ee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee..........hhhhh..ee........ee......ee.....ee....hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh..eeeee......------....hhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1icp A  10 QVDKIPLMSPCKMGKFELCHRVVLAPLTRQRSYGYIPQPHAILHYSQRSTNGGLLIGEATVISETGIGYKDVPGIWTKEQVEAWKPIVDAVHAKGGIFFCQIWHVGRVSNKDFQPNGEDPISCTDRGLTPQIMSNGIDIAHFTRPRRLTTDEIPQIVNEFRVAARNAIEAGFDGVEIHGAHGYLIDQFMKDQVNDRSDKYGGSLENRCRFALEIVEAVANEIGSDRVGIRISPFAHYNEAGDTNPTALGLYMVESLNKYDLAYCHVVEPRMKT------CTESLVPMRKAYKGTFIVAGGYDREDGNRALIEDRADLVAYGRLFISNPDLPKRFELNAPLNKYNRDTFYTSDPIVGYTDYPFLE 373
                                    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       269       279  |    289       299       309       319       329       339       349       359       369    
                                                                                                                                                                                                                                                                                                          282    289

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with OPR1_SOLLC | Q9XG54 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:365
                                    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       269       279       289       299       309       319       329       339       349       359       369     
           OPR1_SOLLC    10 QVDKIPLMSPCKMGKFELCHRVVLAPLTRQRSYGYIPQPHAILHYSQRSTNGGLLIGEATVISETGIGYKDVPGIWTKEQVEAWKPIVDAVHAKGGIFFCQIWHVGRVSNKDFQPNGEDPISCTDRGLTPQIRSNGIDIAHFTRPRRLTTDEIPQIVNEFRVAARNAIEAGFDGVEIHGAHGYLIDQFMKDQVNDRSDKYGGSLENRCRFALEIVEAVANEIGSDRVGIRISPFAHYNEAGDTNPTALGLYMVESLNKYDLAYCHVVEPRMKTAWEKIECTESLVPMRKAYKGTFIVAGGYDREDGNRALIEDRADLVAYGRLFISNPDLPKRFELNAPLNKYNRDTFYTSDPIVGYTDYPFLET 374
               SCOP domains d1icpb_ B: 12-oxophytodienoate reductase (OPR, OYE homolog)                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1icpB00 B:10-374 Aldolase class I                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.eee..eee...eee.......hhhhh.hhhhhhhhhhh.....eee...ee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh..ee........ee......ee.....ee....hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhh..eeeee......-------...hhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1icp B  10 QVDKIPLMSPCKMGKFELCHRVVLAPLTRQRSYGYIPQPHAILHYSQRSTNGGLLIGEATVISETGIGYKDVPGIWTKEQVEAWKPIVDAVHAKGGIFFCQIWHVGRVSNKDFQPNGEDPISCTDRGLTPQIMSNGIDIAHFTRPRRLTTDEIPQIVNEFRVAARNAIEAGFDGVEIHGAHGYLIDQFMKDQVNDRSDKYGGSLENRCRFALEIVEAVANEIGSDRVGIRISPFAHYNEAGDTNPTALGLYMVESLNKYDLAYCHVVEPRMKT-------TESLVPMRKAYKGTFIVAGGYDREDGNRALIEDRADLVAYGRLFISNPDLPKRFELNAPLNKYNRDTFYTSDPIVGYTDYPFLET 374
                                    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       269       279  |      -|      299       309       319       329       339       349       359       369     
                                                                                                                                                                                                                                                                                                          282     290

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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: 12-oxophytodienoate reductase (OPR, OYE homolog) (7)

Tomato (Lycopersicon esculentum), OPR1 [TaxId: 4081] (4)

1a	d1icpa_	A:
1b	d1icpb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Solanum lycopersicum. Organism_taxid: 4081. (6)

1a	1icpA00	A:10-373
1b	1icpB00	B:10-374

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (OPR1_SOLLC | Q9XG54)

molecular function
	GO:0016629	12-oxophytodienoate reductase activity	Catalysis of the reaction: 8-[(1R,2R)-3-oxo-2-{(Z)-pent-2-en-1-yl}cyclopentyl]octanoate + NADP(+) = (15Z)-12-oxophyto-10,15-dienoate + H(+) + NADPH.
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003959	NADPH dehydrogenase activity	Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
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:0031408	oxylipin biosynthetic process	The chemical reactions and pathways resulting in the formation of any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	OPR1_SOLLC \| Q9XG54	:	1icq 1ics 3hgr

1icq	CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-12-OPDA
1ics	CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO

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Ligands, Modified Residues, Ions (4, 7)

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