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(-) Description

Title :  CRYSTAL STRUCTURE OF OLD YELLOW ENZYME MUTANT GLN114ASN COMPLEXED WITH PARA-HYDROXY BENZALDEHYDE
 
Authors :  B. J. Brown, J. Hyun, S. D. Duvvuri, P. A. Karplus, V. Massey
Date :  18 Sep 01  (Deposition) - 26 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha Barrels, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Brown, J. Hyun, S. D. Duvvuri, P. A. Karplus, V. Massey
The Role Of Glutamine 114 In Old Yellow Enzyme
J. Biol. Chem. V. 277 2138 2002
PubMed-ID: 11668181  |  Reference-DOI: 10.1074/JBC.M108453200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADPH DEHYDROGENASE 1
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: OLD YELLOW ENZYME 1, OYE1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2HBA1Ligand/IonP-HYDROXYBENZALDEHYDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:380 , LEU A:392 , HOH A:917 , HOH A:919 , HOH A:920BINDING SITE FOR RESIDUE MG A 405
2AC2SOFTWAREPRO A:35 , LEU A:36 , THR A:37 , GLY A:72 , HIS A:191 , ASN A:194 , ARG A:243 , GLY A:324 , ASN A:325 , GLY A:347 , ARG A:348 , PHE A:374 , TYR A:375 , HBA A:450 , HOH A:528 , HOH A:532 , HOH A:590BINDING SITE FOR RESIDUE FMN A 401
3AC3SOFTWARETHR A:37 , TRP A:116 , HIS A:191 , ASN A:194 , TYR A:196 , PHE A:250 , PHE A:296 , TYR A:375 , FMN A:401BINDING SITE FOR RESIDUE HBA A 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K03)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K03)

(-) Exons   (0, 0)

(no "Exon" information available for 1K03)

(-) Sequences/Alignments

Asymmetric/Biological 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
 aligned with OYE1_SACPS | Q02899 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:399
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391         
           OYE1_SACPS     2 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 400
               SCOP domains d1k03a_ A: Old yellow enzyme (OYE)                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1k03A00 A:1-399 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------Oxidored_FMN-1k03A01 A:15-367                                                                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.eee..eee...eee..................hhhhhhhhh......eeeeeeee...............hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh...eee.......hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeee......................hhhhhh...eeee.....hhhhhhhhh....eeee.hhhhhhh.hhhhhhhhh......hhhhh............hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k03 A   1 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVNLWVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OYE1_SACPS | Q02899)
molecular function
    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.
    GO:0018548    pentaerythritol trinitrate reductase activity    Catalysis of the reaction: pentaerythritol trinitrate + NADPH = NADP+ + nitrate + pentaerythritol dinitrate.
    GO:0052690    trichloro-p-hydroquinone reductive dehalogenase activity    Catalysis of the reaction: 2,3,6-trichlorohydroquinone + 2 glutathione = 2,6-dichlorohydroquinone + glutathione disulfide + HCl.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OYE1_SACPS | Q02899: 1bwk 1bwl 1k02 1oya 1oyb 1oyc 3rnd 3tx9 3txz 4gbu 4ge8 4gwe 4gxm 4h4i 4h6k 4k7v 4k7y 4k8e 4k8h 4rnu 4rnv 4rnw 4rnx 4yil 4ync

(-) Related Entries Specified in the PDB File

1k02 1K02 IS THE CRYSTAL STRUCTURE OF OLD YELLOW ENZYME MUTANT GLN114ASN
1oya 1OYA IS THE CRYSTAL STRUCTURE OF OLD YELLOW ENZYME (OXIDISED)
1oyb 1OYB IS THE CRYSTAL STRUCTURE OF OLD YELLOW ENZYME (OXIDISED) COMPLEXED WITH PARA-HYDROXY BENZALDEHYDE
1oyc 1OYC IS THE CRYSTAL STRUCTURE OF OLD YELLOW ENZYME (REDUCED)