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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF 4-IMIDAZOLONE-5-PROPANOATE AMIDOHYDROLASE FROM ENVIRONMENTAL SAMPLE
 
Authors :  R. Tyagi, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sg Research Center For Structural Genomics (Nysgxrc)
Date :  25 Jan 07  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  9252H, Nysgxrc, 4-Imidazolone-5-Propanoate Amidohydrolase, Psi2_community, Psi-2, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Tyagi, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
The Crystal Structure Of 4-Imidazolone-5-Propanoate Amidohydrolase From Environmental Sample
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-IMIDAZOLONE-5-PROPANOATE AMIDOHYDROLASE
    Chains: A
    EC Number: 3.5.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: T7
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PSGX3(BC)
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:72 , HIS A:74 , HIS A:242 , ASP A:317 , HOH A:701BINDING SITE FOR RESIDUE FE A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:52 -Pro A:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OOF)

(-) 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:403
 aligned with HUTI_AERHH | A0KF84 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:405
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     
           HUTI_AERHH     6 LNCERVWLNVTPATLRSDLADYGLLEPHALGVHEGRIHALVPMQDLKGPYPAHWQDMKGKLVTPGLIDCHTHLIFAGSRAEEFELRQKGVPYAEIARKGGGIISTVRATRAACEEQLFELALPRVKSLIREGVTTVEIKSGYGLTLEDELKMLRVARRLGEALPIRVKTTLLAAHAVPPEYRDDPDSWVETICQEIIPAAAEAGLADAVDVFCEHIGFSLAQTEQVYLAADQYGLAVKGHMDQLSNLGGSTLAANFGALSVDHLEYLDPEGIQALAHRGVVATLLPTAFYFLKETKLPPVAALRKAGVPMAVSSDINPGTAPIVSLRMAMNMACTLFGLTPVEAMAGVTRHAARALGEQEQLGQLRVGMLADFLVWNCGHPAELSYLIGVDQLVSRVINGEETLH 410
               SCOP domains d2oofa1 A:3-65,A:367-407                                       d2oofa2 A:66-366 Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421                                                                                                                                                                                                                              d2oofa1 A:3-65,A:367-407                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------Amidohydro_4-2oofA01 A:58-376                                                                                                                                                                                                                                                                                                  ------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...............eeeeee..eeeeeee.hhh.--.....ee....eeee.eeeeee.......hhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh...eeee....hhhhhhhhhhhh.eeeehhhhhhhh......hhhhhhhh...eee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....hhhhhh.....eeeeee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oof A   3 LNCERVWLNVTPATLRSDLADYGLLEPHALGVHEGRIHALVPmQDLK--YPAHWQDmKGKLVTPGLIDCHTHLIFAGSRAEEFELRQKGVPYAEIARKGGGIISTVRATRAASEDQLFELALPRVKSLIREGVTTVEIKSGYGLTLEDELKmLRVARRLGEALPIRVKTTLLAAHAVPPEYRDDPDSWVETICQEIIPAAAEAGLADAVDVFCEHIGFSLAQTEQVYLAADQYGLAVKGHmDQLSNLGGSTLAANFGALSVDHLEYLDPEGIQALAHRGVVATLLPTAFYFLKETKLPPVVALRKAGVPmAVSSDINPGTAPIVSLRmAmNmACTLFGLTPVEAmAGVTRHAARALGEQEQLGQLRVGmLADFLVWNCGHPAELSYLIGVDQLVSRVVNGEETLH 407
                                    12        22        32        42  |   | 52      | 62        72        82        92       102       112       122       132       142       152 |     162       172       182       192       202       212       222       232       242|      252       262       272       282       292       302       312       322       332 |     342    |  352       362       372       382       392       402     
                                                                     45-MSE 52     59-MSE                                                                                        154-MSE                                                                                  243-MSE                                                              312-MSE           330-MSE          347-MSE                 371-MSE                                
                                                                                                                                                                                                                                                                                                                                                                   332-MSE                                                                       
                                                                                                                                                                                                                                                                                                                                                                     334-MSE
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (HUTI_AERHH | A0KF84)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0016812    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
    GO:0050480    imidazolonepropionase activity    Catalysis of the reaction: (S)-3-(4-oxo-4,5-dihydro-1H-imidazol-5-yl)propanoic acid + H(2)O = N-formimidoyl-L-glutamate + H(+).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006548    histidine catabolic process    The chemical reactions and pathways resulting in the breakdown of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0019556    histidine catabolic process to glutamate and formamide    The chemical reactions and pathways resulting in the breakdown of histidine into other compounds, including glutamate and formamide.
    GO:0019557    histidine catabolic process to glutamate and formate    The chemical reactions and pathways resulting in the breakdown of histidine into other compounds, including glutamate and formate.
    GO:0006547    histidine metabolic process    The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:52 - Pro A:53   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  2oof
    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
  HUTI_AERHH | A0KF84
    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)
  3.5.2.7
    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
  HUTI_AERHH | A0KF84
    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
        HUTI_AERHH | A0KF84: 2q09

(-) Related Entries Specified in the PDB File

2gok CRYSTAL STRUCTURE OF THE IMIDAZOLONEPROPIONASE FROM AGROBACTERIUM TUMEFACIENS AT 1.87 A RESOLUTION