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(-) Description

Title :  STRUCTURE OF IMIDAZOLONEPROPIONASE FROM BACILLUS SUBTILIS
 
Authors :  Y. H. Liang, Y. Yu, X. D. Su
Date :  16 Oct 05  (Deposition) - 26 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yu, Y. H. Liang, E. Brostromer, J. M. Quan, S. Panjikar, Y. H. Dong, X. D. Su
A Catalytic Mechanism Revealed By The Crystal Structures Of The Imidazolonepropionase From Bacillus Subtilis
J. Biol. Chem. V. 281 36929 2006
PubMed-ID: 16990261  |  Reference-DOI: 10.1074/JBC.M607703200

(-) Compounds

Molecule 1 - IMIDAZOLONEPROPIONASE
    Chains: A, B
    EC Number: 3.5.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21-DEST
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: HUTI, IMIDAZOLONE-5-PROPIONATE HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:89 , TYR A:102 , ILE A:112 , TYR A:152 , ASN A:326 , GLY A:328BINDING SITE FOR RESIDUE ACT A 1501
2AC2SOFTWAREARG B:89 , TYR B:102 , ILE B:112 , TYR B:152 , ASN B:326 , GLY B:328BINDING SITE FOR RESIDUE ACT B 2501
3AC3SOFTWAREHIS A:80 , HIS A:82 , HIS A:249 , ASP A:324 , HOH A:1729BINDING SITE FOR RESIDUE ZN A 1601
4AC4SOFTWAREHIS B:80 , HIS B:82 , HIS B:249 , ASP B:324 , HOH B:2714BINDING SITE FOR RESIDUE ZN B 2601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BB0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BB0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BB0)

(-) Exons   (0, 0)

(no "Exon" information available for 2BB0)

(-) 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:413
 aligned with HUTI_BACSU | P42084 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:413
                                    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       412   
           HUTI_BACSU     3 KQIDTILINIGQLLTMESSGPRAGKSMQDLHVIEDAVVGIHEQKIVFAGQKGAEAGYEADEIIDCSGRLVTPGLVDPHTHLVFGGSREKEMNLKLQGISYLDILAQGGGILSTVKDTRAASEEELLQKAHFHLQRMLSYGTTTAEVKSGYGLEKETELKQLRVAKKLHESQPVDLVSTFMGAHAIPPEYQNDPDDFLDQMLSLLPEIKEQELASFADIFTETGVFTVSQSRRYLQKAAEAGFGLKIHADEIDPLGGAELAGKLKAVSADHLVGTSDEGIKKLAEAGTIAVLLPGTTFYLGKSTYARARAMIDEGVCVSLATDFNPGSSPTENIQLIMSIAALHLKMTAEEIWHAVTVNAAYAIGKGEEAGQLKAGRSADLVIWQAPNYMYIPYHYGVNHVHQVMKNGTIVVNR 415
               SCOP domains d2bb0a1 A:3-73,A:374-415 Imidazolonepropionase                         d2bb0a2 A:74-373 Imidazolonepropionase                                                                                                                                                                                                                                                                      d2bb0a1 A:3-73,A:374-415                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.........hhhhhh....eeeeeeeee..eeeeeee.......eeeeeee....eeee.eee..........hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh...eeee....hhhhhhhhhhhh.eeeehhhhhhhh......hhhhhhhh...eee............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh................eeee.....hhhhhh.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bb0 A   3 KQIDTILINIGQLLTMESSGPRAGKSMQDLHVIEDAVVGIHEQKIVFAGQKGAEAGYEADEIIDCSGRLVTPGLVDPHTHLVFGGSREKEMNLKLQGISYLDILAQGGGILSTVKDTRAASEEELLQKAHFHLQRMLSYGTTTAEVKSGYGLEKETELKQLRVAKKLHESQPVDLVSTFMGAHAIPPEYQNDPDDFLDQMLSLLPEIKEQELASFADIFTETGVFTVSQSRRYLQKAAEAGFGLKIHADEIDPLGGAELAGKLKAVSADHLVGTSDEGIKKLAEAGTIAVLLPGTTFYLGKSTYARARAMIDEGVCVSLATDFNPGSSPTENIQLIMSIAALHLKMTAEEIWHAVTVNAAYAIGKGEEAGQLKAGRSADLVIWQAPNYMYIPYHYGVNHVHQVMKNGTIVVNR 415
                                    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       412   


Chain B from PDB  Type:PROTEIN  Length:413
 aligned with HUTI_BACSU | P42084 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:413
                                    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       412   
           HUTI_BACSU     3 KQIDTILINIGQLLTMESSGPRAGKSMQDLHVIEDAVVGIHEQKIVFAGQKGAEAGYEADEIIDCSGRLVTPGLVDPHTHLVFGGSREKEMNLKLQGISYLDILAQGGGILSTVKDTRAASEEELLQKAHFHLQRMLSYGTTTAEVKSGYGLEKETELKQLRVAKKLHESQPVDLVSTFMGAHAIPPEYQNDPDDFLDQMLSLLPEIKEQELASFADIFTETGVFTVSQSRRYLQKAAEAGFGLKIHADEIDPLGGAELAGKLKAVSADHLVGTSDEGIKKLAEAGTIAVLLPGTTFYLGKSTYARARAMIDEGVCVSLATDFNPGSSPTENIQLIMSIAALHLKMTAEEIWHAVTVNAAYAIGKGEEAGQLKAGRSADLVIWQAPNYMYIPYHYGVNHVHQVMKNGTIVVNR 415
               SCOP domains d2bb0b1 B:3-73,B:374-415 Imidazolonepropionase                         d2bb0b2 B:74-373 Imidazolonepropionase                                                                                                                                                                                                                                                                      d2bb0b1 B:3-73,B:374-415                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.........hhhhhh....eeeeeeeee..eeeeeee.......eeeeeee....eeee.eeeeee.......hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhh..ee..ee......hhhhhhhhh...eeee....hhhhhhhhhhhh.eeeehhhhhhhh......hhhhhhhh...eee............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh................eeee.....hhhhhh.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bb0 B   3 KQIDTILINIGQLLTMESSGPRAGKSMQDLHVIEDAVVGIHEQKIVFAGQKGAEAGYEADEIIDCSGRLVTPGLVDPHTHLVFGGSREKEMNLKLQGISYLDILAQGGGILSTVKDTRAASEEELLQKAHFHLQRMLSYGTTTAEVKSGYGLEKETELKQLRVAKKLHESQPVDLVSTFMGAHAIPPEYQNDPDDFLDQMLSLLPEIKEQELASFADIFTETGVFTVSQSRRYLQKAAEAGFGLKIHADEIDPLGGAELAGKLKAVSADHLVGTSDEGIKKLAEAGTIAVLLPGTTFYLGKSTYARARAMIDEGVCVSLATDFNPGSSPTENIQLIMSIAALHLKMTAEEIWHAVTVNAAYAIGKGEEAGQLKAGRSADLVIWQAPNYMYIPYHYGVNHVHQVMKNGTIVVNR 415
                                    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       412
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BB0)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HUTI_BACSU | P42084)
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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        HUTI_BACSU | P42084: 2g3f

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