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(-) Description

Title :  OYE1-W116I COMPLEXED WITH (S)-CARVONE
 
Authors :  Y. A. Pompeu, J. D. Stewart
Date :  01 Aug 12  (Deposition) - 29 Aug 12  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Carvone, Enoate Reductase, Alkene Reductase, Enenatioselectivity, Substrate Flipping, Tim Barrel, Nad(P)H, Oxidoreductase (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

(-) Compounds

Molecule 1 - NADPH DEHYDROGENASE 1
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3B
    Expression System Strain: BL21(DE3) GOLD
    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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
10WU1Ligand/Ion(5S)-2-METHYL-5-(PROP-1-EN-2-YL)CYCLOHEX-2-EN-1-ONE
21PE4Ligand/IonPENTAETHYLENE GLYCOL
3CL3Ligand/IonCHLORIDE ION
4FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
5MG1Ligand/IonMAGNESIUM ION
6NA4Ligand/IonSODIUM ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
10WU2Ligand/Ion(5S)-2-METHYL-5-(PROP-1-EN-2-YL)CYCLOHEX-2-EN-1-ONE
21PE8Ligand/IonPENTAETHYLENE GLYCOL
3CL-1Ligand/IonCHLORIDE ION
4FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
5MG-1Ligand/IonMAGNESIUM ION
6NA-1Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:836 , HOH A:900 , HOH A:918 , HOH A:919 , HOH A:937 , HOH A:938BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREASP A:83 , ASN A:126BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWARELYS A:4 , LYS A:368 , HOH A:916 , HOH A:950BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREALA A:145BINDING SITE FOR RESIDUE CL A 404
05AC5SOFTWARETYR A:375 , 1PE A:409 , HOH A:838BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWAREALA A:10 , 1PE A:410BINDING SITE FOR RESIDUE NA A 406
07AC7SOFTWARETRP A:52 , 1PE A:408 , HOH A:826BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWARETRP A:52 , ASP A:358 , ALA A:379 , GLU A:389 , NA A:407 , HOH A:962BINDING SITE FOR RESIDUE 1PE A 408
09AC9SOFTWARETYR A:82 , PHE A:123 , PHE A:296 , NA A:405 , HOH A:752BINDING SITE FOR RESIDUE 1PE A 409
10BC1SOFTWAREPRO A:8 , GLN A:9 , ALA A:10 , HIS A:43 , ASP A:83 , ASN A:84 , ARG A:334 , LYS A:362 , GLY A:363 , NA A:406 , HOH A:652 , HOH A:858BINDING SITE FOR RESIDUE 1PE A 410
11BC2SOFTWAREPRO 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 , GLY A:324 , ASN A:325 , GLY A:347 , ARG A:348 , PHE A:374 , 0WU A:414 , HOH A:503 , HOH A:504 , HOH A:506 , HOH A:515BINDING SITE FOR RESIDUE FMN A 411
12BC3SOFTWARE1PE A:413BINDING SITE FOR RESIDUE NA A 412
13BC4SOFTWAREASP A:370 , HIS A:380 , ASP A:384 , NA A:412 , HOH A:785BINDING SITE FOR RESIDUE 1PE A 413
14BC5SOFTWARETHR A:37 , TYR A:82 , ILE A:116 , HIS A:191 , ASN A:194 , TYR A:196 , TYR A:375 , FMN A:411BINDING SITE FOR RESIDUE 0WU A 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GE8)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GE8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GE8)

(-) Sequences/Alignments

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 d4ge8a_ 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...............hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh...eee.......hhhhhhhhhhhh..eee.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
                 4ge8 A   1 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLIVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 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)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GE8)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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    His A:43 - Pro A:44   [ RasMol ]  
 
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  OYE1_SACPS | Q02899
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  1.6.99.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OYE1_SACPS | Q02899: 1bwk 1bwl 1k02 1k03 1oya 1oyb 1oyc 3rnd 3tx9 3txz 4gbu 4gwe 4gxm 4h4i 4h6k 4k7v 4k7y 4k8e 4k8h 4rnu 4rnv 4rnw 4rnx 4yil 4ync

(-) Related Entries Specified in the PDB File

3rnd 3tx9 3txz 4gbu 4gwe 4gxm 4h4i 4h6k 4k7v 4k7y 4k8e 4k8h