4K8E - JenaLib

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Title :   OYE1-W116V COMPLEXED WITH THE AROMATIC PRODUCT OF (R)-CARVONE DISMUTATION

Authors :   B. Sullivan, Y. A. Pompeu, J. D. Stewart

Date :   18 Apr 13 (Deposition) - 09 Oct 13 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.27

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

Keywords :   Old Yellow Enzyme, Carvone, Oxidoreductase, Tim-Barrel, Nadph Dehydrogenase 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. A. Pompeu, B. Sullivan, J. D. Stewart
X‑ Ray Crystallography Reveals How Subtle Changes Control The Orientation Of Substrate Binding In An Alkene Reductase
Acs Catalysis V. 3 2376 2013
PubMed: search | Reference-DOI: 10.1021/CS400622E

Molecule 1 - NADPH DEHYDROGENASE 1
	Chains	:	A
	EC Number	:	1.6.99.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3B
	Expression System Strain	:	BL21-GOLD(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	OYE1
	Mutation	:	YES
	Organism Common	:	LAGER YEAST
	Organism Scientific	:	SACCHAROMYCES PASTORIANUS
	Organism Taxid	:	27292
	Synonym	:	OLD YELLOW ENZYME 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 15)

No.	Name	Count	Type	Full Name
1	0WV	1	Ligand/Ion	2-METHYL-5-(PROP-1-EN-2-YL)PHENOL
2	CL	2	Ligand/Ion	CHLORIDE ION
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	NA	4	Ligand/Ion	SODIUM ION
6	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
7	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	0WV	2	Ligand/Ion	2-METHYL-5-(PROP-1-EN-2-YL)PHENOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION
6	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
7	PGE	8	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:34 , PRO A:35 , LEU A:36 , THR A:37 , GLY A:72 , GLN A:114 , HIS A:191 , ASN A:194 , ARG A:243 , PRO A:295 , GLY A:324 , ASN A:325 , GLY A:347 , ARG A:348 , 0WV A:404 , CL A:406 , HOH A:503 , HOH A:504 , HOH A:509 , HOH A:510	BINDING SITE FOR RESIDUE FMN A 401
02	AC2	SOFTWARE	HOH A:1001 , HOH A:1053 , HOH A:1054 , HOH A:1055	BINDING SITE FOR RESIDUE MG A 402
03	AC3	SOFTWARE	ASP A:83 , ASN A:126	BINDING SITE FOR RESIDUE CL A 403
04	AC4	SOFTWARE	THR A:37 , TYR A:82 , HIS A:191 , ASN A:194 , TYR A:196 , TYR A:375 , FMN A:401	BINDING SITE FOR RESIDUE 0WV A 404
05	AC5	SOFTWARE	HOH A:880 , HOH A:1014 , HOH A:1015 , HOH A:1037 , HOH A:1071 , HOH A:1072	BINDING SITE FOR RESIDUE MG A 405
06	AC6	SOFTWARE	HIS A:191 , ASN A:194 , TYR A:196 , FMN A:401	BINDING SITE FOR RESIDUE CL A 406
07	AC7	SOFTWARE	ASP A:370 , HIS A:380 , ASP A:384 , HOH A:902 , HOH A:912 , HOH A:1100 , HOH A:1142	BINDING SITE FOR RESIDUE PEG A 407
08	AC8	SOFTWARE	TRP A:52 , PGE A:415	BINDING SITE FOR RESIDUE NA A 408
09	AC9	SOFTWARE	GLN A:9 , ALA A:10 , HIS A:43 , ASP A:83 , ARG A:129 , ARG A:334 , LYS A:362 , GLY A:363 , NA A:410	BINDING SITE FOR RESIDUE PGE A 409
10	BC1	SOFTWARE	GLN A:9 , ALA A:10 , PGE A:409	BINDING SITE FOR RESIDUE NA A 410
11	BC2	SOFTWARE	TYR A:375 , PGE A:412 , HOH A:939	BINDING SITE FOR RESIDUE NA A 411
12	BC3	SOFTWARE	PHE A:123 , PHE A:296 , TYR A:375 , NA A:411	BINDING SITE FOR RESIDUE PGE A 412
13	BC4	SOFTWARE	PGE A:414 , HOH A:631	BINDING SITE FOR RESIDUE NA A 413
14	BC5	SOFTWARE	GLU A:305 , GLY A:307 , SER A:308 , TYR A:313 , ASP A:339 , NA A:413 , HOH A:993	BINDING SITE FOR RESIDUE PGE A 414
15	BC6	SOFTWARE	ASP A:51 , TRP A:52 , ASP A:358 , GLU A:389 , NA A:408 , HOH A:945	BINDING SITE FOR RESIDUE PGE A 415

(no "SS Bond" information available for 4K8E)

Asymmetric Unit

No.	Residues
1	His A:43	-	Pro A:44

(no "SAP(SNP)/Variant" information available for 4K8E)

(no "PROSITE Motif" information available for 4K8E)

(no "Exon" information available for 4K8E)

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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k8ea_ A: Old yellow enzyme (OYE)                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.eee..eee...ee...................hhhhhhhhhh.....eee...ee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh....ee.......hhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeee.....................hhhhhhh...eeee.....hhhhhhhhh....eeee.hhhhhhh.hhhhhhhhh......hhhhh............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8e A   1 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLVVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 399
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

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: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: Old yellow enzyme (OYE) (20)

Lager yeast (Saccharomyces pastorianus) [TaxId: 27292] (18)

d4k8ea_

(no "CATH Domain" information available for 4K8E)

(no "Pfam Domain" information available for 4K8E)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		0WV	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC7	[ RasMol ]	+environment [ RasMol ]
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		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
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		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His A:43 - Pro A:44	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	4k8e
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	OYE1_SACPS \| Q02899
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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Access by Enzyme Classificator (EC Number)
	1.6.99.1
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		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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3rnd
3tx9
3txz	OYE1-W116Q COMPLEXED WITH (R)-CARVONE
4gbu	OYE1-W116A COMPLEXED WITH THE AROMATIC PRODUCT OF (S)- CARVONE DISMUTATION
4ge8	OYE1-W116I COMPLEXED WITH (S)-CARVONE
4gwe	OYE1-W116L COMPLEXED WITH (R)-CARVONE
4gxm	OYE1-W116L COMPLEXED WITH THE AROMATIC PRODUCT OF (R)- CARVONE DISMUTATION
4h4i	OYE1-W116V COMPLEXED WITH THE AROMATIC PRODUCT OF (S)- CARVONE DISMUTATION
4h6k	OYE1-W116I
4k7v	OYE1-W116A COMPLEXED WITH (R)-CARVONE
4k7y	OYE1-W116T
4k8h	OYE1-W116V COMPLEXED WITH (R)-CARVONE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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