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(-) Description

Title :  CRYSTAL STRUCTURE OF IMIDAZOLONEPROPIONASE FROM AGROBACTERIUM TUMEFACIENS WITH BOUND PRODUCT N-FORMIMINO-L-GLUTAMATE
 
Authors :  R. Tyagi, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sg Research Center For Structural Genomics (Nysgxrc)
Date :  09 May 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nysgxrc, 9252B, Psi-2, Imidazolonepropionase, N-Formimino-L- Glutamate, Product-Bound, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Tyagi, D. Kumaran, S. K. Burley, S. Swaminathan
X-Ray Structure Of Imidazolonepropionase From Agrobacterium Tumefaciens At 1. 87 A Resolution.
Proteins V. 69 652 2007
PubMed-ID: 17640072  |  Reference-DOI: 10.1002/PROT.21559

(-) Compounds

Molecule 1 - IMIDAZOLONEPROPIONASE
    Atcc: 33970
    Chains: A, B
    EC Number: 3.5.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HUTI, ATU3934, AGR_L_1824
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: IMIDAZOLONE-5-PROPIONATE HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FE2Ligand/IonFE (III) ION
3MG1Ligand/IonMAGNESIUM ION
4NIG1Ligand/IonN-(IMINOMETHYL)-L-GLUTAMIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:256 , ASP A:331 , HOH A:640BINDING SITE FOR RESIDUE FE A 500
2AC2SOFTWAREHIS B:86 , HIS B:88 , HIS B:256 , ASP B:331 , NIG B:600 , HOH B:1183BINDING SITE FOR RESIDUE FE B 501
3AC3SOFTWAREASP A:203 , HOH A:725 , HOH A:732 , ASP B:393 , HOH B:655 , HOH B:745BINDING SITE FOR RESIDUE MG B 502
4AC4SOFTWAREARG A:200 , ALA A:202 , ASP A:203BINDING SITE FOR RESIDUE CL B 504
5AC5SOFTWAREHIS B:88 , ARG B:95 , TYR B:158 , HIS B:191 , PHE B:228 , ILE B:232 , ASN B:333 , GLY B:335 , THR B:336 , FE B:501 , HOH B:790 , HOH B:804 , HOH B:1183 , HOH B:1184BINDING SITE FOR RESIDUE NIG B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PUZ)

(-) 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:404
 aligned with HUTI_AGRFC | Q8U8Z6 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:404
                                    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    
           HUTI_AGRFC    15 ATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVS 418
               SCOP domains d2puza1 A:17-79,A:381-420 Imidazolonepropionase                d2puza2 A:80-380 Imidazolonepropionase                                                                                                                                                                                                                                                                       d2puza1 A:17-79,A:381-420                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..........eeeeeeeeee..eeeeeee....hhhhh...eeee....eeee.eee..........hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhh.....eeeeee......hhhhh.hhhhhhhhhhhhhhhhhhhh....ee..ee.....hhhhhhhhhhhhhhh....eeee......hhhhhhhhh...eeee....hhhhhhhhhhhh.eeeehhhhhhhhh.....hhhhhhhhh..eee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....hhhhhh.....eeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2puz A  17 ATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVS 420
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416    


Chain B from PDB  Type:PROTEIN  Length:404
 aligned with HUTI_AGRFC | Q8U8Z6 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:404
                                    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    
           HUTI_AGRFC    15 ATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVS 418
               SCOP domains d2puzb1 B:17-79,B:381-420 Imidazolonepropionase                d2puzb2 B:80-380 Imidazolonepropionase                                                                                                                                                                                                                                                                       d2puzb1 B:17-79,B:381-420                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..........eeeeeeeeee..eeeeeee.hhhhhhhh...eeee....eeee.eee..........hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee......hhhhh.hhhhhhhhhhhhhhhhhhhh....ee..ee.....hhhhhhhhhhhhhhh....eeee......hhhhhhhhh...eeee....hhhhhhhhhhhh.eeeehhhhhhhh......hhhhhhhhh..eee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....hhhhhh.....eeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2puz B  17 ATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVS 420
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PUZ)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HUTI_AGRFC | Q8U8Z6)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HUTI_AGRFC | Q8U8Z6: 2gok

(-) Related Entries Specified in the PDB File

2gok CRYSTAL STRUCTURE OF NATIVE IMIDAZOLONEPROPIONASE FROM AGROBACTERIUM TUMEFACIENS
2oof CRYSTAL STRUCTURE OF NATIVE 4-IMIDAZOLONE-5-PROPIONATE AMIDOHYDROLASE FROM ENVIRONMENTAL SAMPLE