Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXIDIZED SHEWANELLA YELLOW ENZYME 1 (SYE1) M25L MUTANT IN COMPLEX WITH PARA-CHLOROPHENOL
 
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 :  1.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (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 - OXIDOREDUCTASE, FMN-BINDING
    ChainsA
    EC Number1.6.99.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPACYC-DUET1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificSHEWANELLA ONEIDENSIS
    Organism Taxid211586
    StrainMR-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
14CH3Ligand/Ion4-CHLOROPHENOL
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4SO41Ligand/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 , PHE A:350 , 4CH A:502 , HOH A:2300 , HOH A:2304 , HOH A:2331 , HOH A:2334 , HOH A:2336BINDING SITE FOR RESIDUE FMN A 500
2AC2SOFTWAREARG A:301 , ARG A:323 , GLU A:333 , ARG A:336 , HIS A:337 , HIS A:344 , HOH A:2361 , HOH A:2375BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWARETHR A:26 , HIS A:181 , ASN A:184 , TYR A:186 , PHE A:350 , FMN A:500BINDING SITE FOR RESIDUE 4CH A 502
4AC4SOFTWARESER A:28 , TYR A:68 , ALA A:69 , TRP A:70 , PHE A:132 , PHE A:142 , PHE A:350BINDING SITE FOR RESIDUE 4CH A 503
5AC5SOFTWAREARG A:84 , GLU A:88 , ILE A:249 , THR A:253 , SER A:283 , ALA A:287 , HOH A:2403BINDING SITE FOR RESIDUE 4CH A 504
6AC6SOFTWAREILE A:43 , ALA A:46 , LYS A:93BINDING SITE FOR RESIDUE PE4 A 505

(-) SS Bonds  (0, 0)

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

(-) 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 4AWU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AWU)

(-) 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 d4awua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee..eee...eee...............hhhhhhhhhhh....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhh.....ee.........eeee.......eeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh....eee.hhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4awu 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    

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4CH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PE4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:32 - Pro A:33   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4awu
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8EEC8_SHEON | Q8EEC8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.6.99.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q8EEC8_SHEON | Q8EEC8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8EEC8_SHEON | Q8EEC82gou 2gq8 2gq9 2gqa 4aws 4awt

(-) 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 , INCOMPLEX WITH P-HYDROXYBENZALDEHYDE
2gqa STRUCTURE OF NADH-REDUCED SYE1, AN OYE HOMOLOGUE FROM S.ONEIDENSIS