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 :  THE HIGH RESOLUTION STRUCTURE OF UROCANATE HYDRATASE FROM PSEUDOMONAS PUTIDA IN COMPLEX WITH UROCANATE
 
Authors :  D. Kessler, J. Retey, G. E. Schulz
Date :  05 Feb 04  (Deposition) - 19 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Urocanase, Imidazolonepropionate, Histidine Metabolism, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kessler, J. Retey, G. E. Schulz
Structure And Action Of Urocanase
J. Mol. Biol. V. 342 183 2004
PubMed-ID: 15313616  |  Reference-DOI: 10.1016/J.JMB.2004.07.028

(-) Compounds

Molecule 1 - UROCANATE HYDRATASE
    Chains: A, B
    EC Number: 4.2.1.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Other Details: CONTAINING NAD+ AND UROCANATE
    Synonym: UROCANASE, IMIDAZOLONEPROPIONATE HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2URO2Ligand/Ion(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:44 , TYR A:52 , GLY A:53 , GLY A:54 , GLN A:131 , ILE A:145 , GLY A:176 , GLY A:177 , MET A:178 , GLY A:179 , GLU A:197 , SER A:198 , GLN A:199 , ARG A:202 , GLY A:242 , ASN A:243 , ALA A:244 , GLN A:264 , THR A:265 , SER A:266 , HIS A:268 , GLY A:273 , TYR A:274 , LEU A:275 , TRP A:281 , TYR A:323 , GLY A:324 , ASN A:325 , PHE A:345 , LEU A:445 , GLY A:493 , HOH A:2428 , HOH A:2429 , HOH A:2430 , HOH A:2431 , URO B:1559 , HOH B:2405BINDING SITE FOR RESIDUE NAD A1558
2AC2SOFTWAREHOH A:2432 , HOH A:2433 , HOH A:2434 , TYR B:52 , GLN B:131 , MET B:132 , THR B:133 , TYR B:139 , GLY B:144 , MET B:178 , ARG B:362 , ASP B:443 , GLY B:493 , NAD B:1558 , HOH B:2333BINDING SITE FOR RESIDUE URO A1559
3AC3SOFTWAREURO A:1559 , HOH A:2433 , GLU B:44 , TYR B:52 , GLY B:53 , GLY B:54 , GLN B:131 , ILE B:145 , GLY B:176 , GLY B:177 , MET B:178 , GLY B:179 , GLU B:197 , SER B:198 , GLN B:199 , ARG B:202 , GLY B:242 , ASN B:243 , ALA B:244 , GLN B:264 , THR B:265 , SER B:266 , HIS B:268 , GLY B:273 , TYR B:274 , LEU B:275 , TYR B:323 , GLY B:324 , ASN B:325 , PHE B:345 , LEU B:445 , GLY B:493 , HOH B:2034 , HOH B:2403 , HOH B:2404BINDING SITE FOR RESIDUE NAD B1558
4AC4SOFTWARETYR A:52 , GLN A:131 , MET A:132 , THR A:133 , TYR A:139 , GLY A:144 , ILE A:145 , MET A:178 , ARG A:362 , ASP A:443 , NAD A:1558 , HOH A:2355 , HOH B:2405 , HOH B:2406BINDING SITE FOR RESIDUE URO B1559

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UWK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UWK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UWK)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROCANASEPS01233 Urocanase signature.HUTU_PSEPU442-457
 		  2A:442-457
B:442-457

(-) Exons   (0, 0)

(no "Exon" information available for 1UWK)

(-) 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:554
 aligned with HUTU_PSEPU | P25080 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:554
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553    
           HUTU_PSEPU     4 NNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAMLDFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLDLPMITG 557
               SCOP domains d1uwka_ A: Urocanate hydratase HutU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------1uwkA02 A:142-349 Urocanase like domains                                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh.......hhh.eee...ee...hhhhhhhhhhhhhhh...eeeeee..eeeeeee.......eeeee...hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee..hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh....ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhh.hhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhh......eeeee.......ee................hhhhhhhhhhhhhhh..eeeeee.........eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UROCANASE       ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uwk A   4 NNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGSLKGKWVLTAGLGGMGGAQPLAATLAGACSLNIESQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAMLDFQKQGVPTFDYGNNIRQMAKEEGVADAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNAETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLDLPMITG 557
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553    


Chain B from PDB  Type:PROTEIN  Length:553
 aligned with HUTU_PSEPU | P25080 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:553
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554   
           HUTU_PSEPU     5 NKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAMLDFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLDLPMITG 557
               SCOP domains d1uwkb_ B: Urocanate hydratase HutU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------1uwkB02 B:142-349 Urocanase like domains                                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Urocanase-1uwkB01 B:11-556                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) ------Urocanase-1uwkB02 B:11-556                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhhhhh.......hhh.eee...ee...hhhhhhhhhhhhhhh...eeeeee..eeeeeee.......eeeee...hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee..hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.....ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhh.hhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhh......eeeee.......ee................hhhhhhhhhhhhhhh..eeeeee.........eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UROCANASE       ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uwk B   5 NKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGSLKGKWVLTAGLGGMGGAQPLAATLAGACSLNIESQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAMLDFQKQGVPTFDYGNNIRQMAKEEGVADAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNAETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLDLPMITG 557
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Urocanase] (5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HUTU_PSEPU | P25080)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0016153    urocanate hydratase activity    Catalysis of the reaction: 4-imidazolone-5-propanoate + H(+) = trans-urocanate + H(2)O.
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/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
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    URO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uwk)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1uwk
    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
  HUTU_PSEPU | P25080
    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)
  4.2.1.49
    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
  HUTU_PSEPU | P25080
    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
        HUTU_PSEPU | P25080: 1uwl 1w1u 2v7g

(-) Related Entries Specified in the PDB File

1uwl 1.76A STRUCTURE OF UROCANATE HYDRATASE FROM PSEUDOMONAS PUTIDA
1w1u INACTIVE UROCANASE-SA COCRYSTALLIZED WITH UROCANATE