Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT OF HPAB (T198I, A276G, AND R466H) COMPLEXED WITH FAD AND 4-HYDROXYPHENYLACETATE
 
Authors :  S. -H. Kim, T. Hisano, K. Takeda, W. Iwasaki, A. Ebihara, K. Miki
Date :  30 Apr 07  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structurome, Riken Spring-8 Center, Oxygnase Component, 4- Hydroxyphenylacetate 3-Monooxygenase, Two-Component Flavin Diffusible Monooxygenase, Mutant, Fad And 4-Hydroxyphenylacetate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -H. Kim, T. Hisano, K. Takeda, W. Iwasaki, A. Ebihara, K. Miki
Crystal Structure Of The Oxygenase Component (Hpab) Of The 4-Hydroxyphenylacetate 3-Monooxygenase From Thermus Thermophilus Hb8
J. Biol. Chem. V. 282 33107 2007
PubMed-ID: 17804419  |  Reference-DOI: 10.1074/JBC.M703440200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4-HYDROXYPHENYLACETATE-3-HYDROXYLASE
    Chains: A
    EC Number: 1.14.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
14HP1Ligand/Ion4-HYDROXYPHENYLACETATE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
14HP4Ligand/Ion4-HYDROXYPHENYLACETATE
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO412Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:73 , TYR A:130 , ARG A:131BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWARETRP A:336 , THR A:337 , ARG A:338 , GLU A:340 , HOH A:1241BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWARETYR A:132 , GLU A:260 , ARG A:261BINDING SITE FOR RESIDUE SO4 A 602
4AC4SOFTWAREARG A:100 , HIS A:142 , ALA A:143 , LEU A:144 , GLN A:148 , ARG A:151 , THR A:183 , THR A:185 , ALA A:312 , TYR A:315 , HIS A:317 , GLN A:378 , ILE A:379 , ALA A:381 , SER A:382 , ARG A:433 , LEU A:436 , TYR A:437 , PHE A:440 , PHE A:441 , GLY A:443 , ASP A:444 , ARG A:447 , 4HP A:550 , HOH A:1015 , HOH A:1037 , HOH A:1049 , HOH A:1067 , HOH A:1104 , HOH A:1143 , HOH A:1201 , HOH A:1441BINDING SITE FOR RESIDUE FAD A 500
5AC5SOFTWAREARG A:100 , TYR A:104 , HIS A:142 , LEU A:144 , SER A:197 , ILE A:198 , LEU A:199 , PHE A:441 , PHE A:442 , FAD A:500 , HOH A:1067BINDING SITE FOR RESIDUE 4HP A 550

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YYM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YYM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YYM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YYM)

(-) Exons   (0, 0)

(no "Exon" information available for 2YYM)

(-) 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:476
 aligned with HPAB_THET8 | Q5SJP8 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:476
                                    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       401       411       421       431       441       451       461       471      
           HPAB_THET8     2 ARTGAEYIEALKTRPPNLWYKGEKVEDPTTHPVFRGIVRTMAALYDLQHDPRYREVLTYEEEGKRHGMSFLIPKTKEDLKRRGQAYKLWADQNLGMMGRSPDYLNAVVMAYAASADYFGEFAENVRNYYRYLRDQDLATTHALTNPQVNRARPPSGQPDPYIPVGVVKQTEKGIVVRGARMTATFPLADEVLIFPSTLLQAGSEKYALAFALPTSTPGLHFVCREALVGGDSPFDHPLSSRVEEMDCLVIFDDVLVPWERVFILGNVELCNNAYAATGALNHMAHQVVALKTAKTEAFLGVAALMAEGIGADVYGHVQEKIAEIIVYLEAMRAFWTRAEEEAKENAYGLLVPDRGALDGARNLYPRLYPRIREILEQIGASGLITLPSEKDFKGPLGPFLEKFLQGAALEAKERVALFRLAWDMTLSGFGARQELYERFFFGDPVRMYQTLYNVYNKEPYKERIRAFLKESLKVFE 477
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --HpaB_N-2yymA02 A:4-264                                                                                                                                                                                                                                               ----HpaB-2yymA01 A:269-471                                                                                                                                                                                     ------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eee..ee.........hhhhhhhhhhhhhhh....hhhhheeee..eeee.hhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...........hhhhh.......eeeee...eeeeeeeeeeee.....eeee..............eeeeee.....eeeee......................eeeeeeeeeeee...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yym A   2 ARTGAEYIEALKTRPPNLWYKGEKVEDPTTHPVFRGIVRTMAALYDLQHDPRYREVLTYEEEGKRHGMSFLIPKTKEDLKRRGQAYKLWADQNLGMMGRSPDYLNAVVMAYAASADYFGEFAENVRNYYRYLRDQDLATTHALTNPQVNRARPPSGQPDPYIPVGVVKQTEKGIVVRGARMTATFPLADEVLIFPSILLQAGSEKYALAFALPTSTPGLHFVCREALVGGDSPFDHPLSSRVEEMDCLVIFDDVLVPWERVFILGNVELCNNAYGATGALNHMAHQVVALKTAKTEAFLGVAALMAEGIGADVYGHVQEKIAEIIVYLEAMRAFWTRAEEEAKENAYGLLVPDRGALDGARNLYPRLYPRIREILEQIGASGLITLPSEKDFKGPLGPFLEKFLQGAALEAKERVALFRLAWDMTLSGFGARQELYERFFFGDPVRMYQTLYNVYNKEPYKERIHAFLKESLKVFE 477
                                    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       401       411       421       431       441       451       461       471
   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 2YYM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YYM)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Acyl-CoA_dh (32)
(-)
Clan: no clan defined [family: HpaB_N] (7)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (HPAB_THET8 | Q5SJP8)
molecular function
    GO:0052881    4-hydroxyphenylacetate 3-monooxygenase activity    Catalysis of the reaction: (4-hydroxyphenyl)acetate + FADH(2) + O(2) = 3,4-dihydroxyphenylacetate + FAD + H(+) + H(2)O.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016712    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
    GO:0010124    phenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylacetate.

 Visualization

(-) Interactive Views

Asymmetric 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
    4HP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yym)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yym
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HPAB_THET8 | Q5SJP8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.13.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HPAB_THET8 | Q5SJP8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HPAB_THET8 | Q5SJP8: 2yyg 2yyi 2yyj 2yyk 2yyl

(-) Related Entries Specified in the PDB File

2yyg LIGAND-FREE FORM OF HPAB
2yyi THE SAME PROTEIN (HPAB) COMPLEXED WITH FAD
2yyj THE SAME PROTEIN (HPAB) COMPLEXED WITH FAD AND 4- HYDROXYPHENYLACETATE
2yyk THE MUTANT OF HPAB
2yyl THE MUTANT OF HPAB COMPLEXED WITH FAD