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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXIDIZED SHEWANELLA YELLOW ENZYME 1 (SYE1) M25L MUTANT
 
Authors :  J. Elegheert, A. Brige, S. N. Savvides
Date :  05 Jun 12  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cofactor-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Elegheert, E. Pauwels, G. Wille, A. Brige, S. N. Savvides
Modulation Of Isoalloxazine Ring Planarity Influences Fmn Electronic Properties In Old Yellow Enzymes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SYE1
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC-DUET1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Other Details: N-TERMINAL T2 IS INVOLVED IN AN N, O FIVE RING ACETAL BY REACTION WITH HO-CH2-CH2-O-CH2-CHO, A PEG400 BREAKDOWN PRODUCT.
    Strain: MR-1
    Synonym: OXIDOREDUCTASE, FMN-BINDING

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric/Biological Unit (6, 7)
No.NameCountTypeFull Name
101F1Ligand/IonETHYL HYDROGEN CARBONATE
2BOG2Ligand/IonB-OCTYLGLUCOSIDE
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
5SL51Mod. Amino Acid(2S,4S,5R)-2-[(2-HYDROXYETHOXY)METHYL]-5-METHYL-1,3-OXAZOLIDINE-4-CARBOXYLIC ACID
6SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:23 , PRO A:24 , LEU A:25 , THR A:26 , GLY A:58 , GLN A:100 , HIS A:181 , ARG A:233 , VAL A:272 , TRP A:274 , GLY A:300 , ARG A:301 , GLY A:322 , ARG A:323 , HOH A:2340 , HOH A:2430 , HOH A:2467 , HOH A:2471 , HOH A:2473BINDING SITE FOR RESIDUE FMN A 500
2AC2SOFTWAREARG A:301 , ARG A:323 , ARG A:336 , HIS A:337 , HIS A:344 , HOH A:2431 , HOH A:2435 , HOH A:2502 , HOH A:2515 , HOH A:2523BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWAREHIS A:39 , ILE A:43 , ALA A:257 , ASN A:260 , LYS A:261 , GLU A:354 , HOH A:2415 , HOH A:2552 , HOH A:2553BINDING SITE FOR RESIDUE BOG A 502
4AC4SOFTWAREALA A:42 , ILE A:43 , GLN A:47 , LYS A:93 , HOH A:2116 , HOH A:2118 , HOH A:2193 , HOH A:2537 , HOH A:2542BINDING SITE FOR RESIDUE BOG A 503
5AC5SOFTWAREGLY A:205 , SER A:206 , ARG A:210 , HOH A:2352 , HOH A:2555 , HOH A:2556BINDING SITE FOR RESIDUE 01F A 504
6AC6SOFTWARETYR A:68 , TYR A:186 , TRP A:274 , HIS A:337 , TYR A:339 , PHE A:350 , HOH A:2034 , HOH A:2508 , HOH A:2557 , HOH A:2558 , HOH A:2559 , HOH A:2560 , HOH A:2561BINDING SITE FOR RESIDUE PE4 A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:32 -Pro A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AWS)

(-) 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:364
 aligned with Q8EEC8_SHEON | Q8EEC8 from UniProtKB/TrEMBL  Length:365

    Alignment length:364
                                    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    
         Q8EEC8_SHEON     2 TQSLFQPITLGALTLKNRIVMPPMTRSRASQPGDVANHMMAIYYAQRASAGLIVSEGTQISPTAKGYAWTPGIYTPEQIAGWRIVTEAVHAKGCAIFAQLWHVGRVTHPDNIDGQQPISSSTLKAENVKVFVDNGSDEPGFVDVAVPRAMTKADIAQVIADYRQAALNAMEAGFDGIELHAANGYLINQFIDSEANNRSDEYGGSLENRLRFLDEVVAALVDAIGAERVGVRLAPLTTLNGTVDADPILTYTAAAALLNKHRIVYLHIAEVDWDDAPDTPVSFKRALREAYQGVLIYAGRYNAEKAEQAINDGLADMIGFGRPFIANPDLPERLRHGYPLAEHVPATLFGGGEKGLTDYPTYQA 365
               SCOP domains d4awsa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee..eee...eee...............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhh.....ee.........eeee.......eeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh....eee.hhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aws A   2 tQSLFQPITLGALTLKNRIVMPPLTRSRASQPGDVANHMMAIYYAQRASAGLIVSEGTQISPTAKGYAWTPGIYTPEQIAGWRIVTEAVHAKGCAIFAQLWHVGRVTHPDNIDGQQPISSSTLKAENVKVFVDNGSDEPGFVDVAVPRAMTKADIAQVIADYRQAALNAMEAGFDGIELHAANGYLINQFIDSEANNRSDEYGGSLENRLRFLDEVVAALVDAIGAERVGVRLAPLTTLNGTVDADPILTYTAAAALLNKHRIVYLHIAEVDWDDAPDTPVSFKRALREAYQGVLIYAGRYNAEKAEQAINDGLADMIGFGRPFIANPDLPERLRHGYPLAEHVPATLFGGGEKGLTDYPTYQA 365
                            |       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    
                            |                                                                                                                                                                                                                                                                                                                                                                           
                            2-SL5
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8EEC8_SHEON | Q8EEC8)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        Q8EEC8_SHEON | Q8EEC8: 2gou 2gq8 2gq9 2gqa 4awt 4awu

(-) Related Entries Specified in the PDB File

2gou STRUCTURE OF WILD TYPE, OXIDIZED SYE1, AN OYE HOMOLOGUEFROM S. ONEIDENSIS
2gq8 STRUCTURE OF SYE1, AN OYE HOMOLOGUE FROM S. ONDEIDENSIS, INCOMPLEX WITH P-HYDROXYACETOPHENONE
2gq9 STRUCTURE OF SYE1, AN OYE HOMOLOGUE FROM S. ONEIDENSIS, IN COMPLEX WITH P-HYDROXYBENZALDEHYDE
2gqa STRUCTURE OF NADH-REDUCED SYE1, AN OYE HOMOLOGUE FROM S.ONEIDENSIS
4awt CRYSTAL STRUCTURE OF THE REDUCED SHEWANELLA YELLOW ENZYME 1 (SYE1) M25L MUTANT
4awu CRYSTAL STRUCTURE OF THE OXIDIZED SHEWANELLA YELLOW ENZYME 1 (SYE1) M25L MUTANT IN COMPLEX WITH PARA- CHLOROPHENOL