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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED SHEWANELLA YELLOW ENZYME 4 (SYE4)
 
Authors :  J. Elegheert, A. Brige, S. N. Savvides
Date :  07 Aug 12  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cofactor-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Elegheert, A. Brige, D. Van Den Hemel, J. Van Beeumena, S. N. Savvides
Structural Basis For The Substrate Promiscuity Of The Old Yellow Enzyme Homologue Sye4 From Shewanella Oneidensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, FMN-BINDING
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC-DUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SHEWANELLA ONEIDENSIS MR-1
    Organism Taxid: 211586
    Synonym: SHEWANELLA YELLOW ENZYME 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
18K61Ligand/IonOCTADECANE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:32 , PRO A:33 , LEU A:34 , THR A:35 , ALA A:66 , GLN A:108 , HIS A:182 , ASN A:185 , ARG A:234 , ILE A:272 , PHE A:273 , VAL A:301 , SER A:303 , GLY A:324 , ARG A:325 , LEU A:351 , 8K6 A:401 , HOH A:2308 , HOH A:2440 , HOH A:2447 , HOH A:2493BINDING SITE FOR RESIDUE FMN A 400
2AC2SOFTWAREALA A:39 , ASP A:40 , ALA A:41 , ASN A:42 , ASN A:78 , TYR A:240 , PHE A:241 , FMN A:400 , HOH A:2180 , HOH A:2375BINDING SITE FOR RESIDUE 8K6 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B5N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5N)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5N)

(-) 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:354
 aligned with Q8EBV3_SHEON | Q8EBV3 from UniProtKB/TrEMBL  Length:355

    Alignment length:354
                                    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    
         Q8EBV3_SHEON     2 TIENTVNSVENLFDTYKLNDTITLKNRILMAPLTRCMADANLVPTDDMVAYYARRAEAGLIISEATIIRPDAQGYPNTPGIFTQAQIAGWRKVTDAVHANGGKIFVQLWHTGRVAHPHFFGGGDVLAPSAQKIEGSVPRMRELTYVTPKAVTVEDIQGLVRDYAKAAENAIEAGFDGVEIHGANGYLIDQFLHHDSNRRTDEYGGTPVNMSRFALEVVDAIIARIGHDRTGLRISPGAYFNMASDSRDRVVFDYLLPELEKRDLAFVHIGIFDDSIEFDYLGGTASSYVRAHYGKTLVGVGSYSAETASKAIAEDKFDLIAIGRPFIANPDYVAKVRNSEELVAYSDEMLASLI 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.ee.....ee...eee..............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....ee.....................ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeee.......eehhhheehhhhhhhhh...eee....hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4b5n A   2 TIENTVNSVENLFDTYKLNDTITLKNRILMAPLTRCMADANLVPTDDMVAYYARRAEAGLIISEATIIRPDAQGYPNTPGIFTQAQIAGWRKVTDAVHANGGKIFVQLWHTGRVAHPHFFGGGDVLAPSAQKIEGSVPRMRELTYVTPKAVTVEDIQGLVRDYAKAAENVIEAGFDGVEIHGANGYLIDQFLHHDSNRRTDEYGGTPVNMSRFALEVVDAIIARIGHDRTGLRISPGAYFNMASDSRDRVVFDYLLPELEKRDLAFVHIGIFDDSIEFDYLGGTASSYVRAHYGKTLVGVGSYSAETASKAIAEDKFDLIAIGRPFIANPDYVAKVRNSEELVAYSDEMLASLI 355
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4B5N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B5N)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8EBV3_SHEON | Q8EBV3)
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.
    GO:0042602    riboflavin reductase (NADPH) activity    Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+.
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

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

UniProtKB/Swiss-Prot
        Q8EBV3_SHEON | Q8EBV3: 5k0r 5k1k 5k1m 5k1q 5k1u 5k1w

(-) Related Entries Specified in the PDB File

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