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(-) Description

Title :  CRYSTAL STRUCTURE OF IMIDAZOLONEPROPIONASE FROM ENVIRONMENTAL SAMPLE WITH BOUND INHIBITOR 3-(2,5-DIOXO-IMIDAZOLIDIN-4-YL)-PROPIONIC ACID
 
Authors :  R. Tyagi, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sg Research Center For Structural Genomics (Nysgxrc)
Date :  21 May 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  9252H, Nysgxrc, Imidazolonepropionase, 3-(2, 5-Dioxo-Imidazolidin- 4Yl)-Propionic Acid, Psi-2 Community, 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, F. M. Raushel, S. Swaminatha
A Common Catalytic Mechanism For Proteins Of The Huti Family.
Biochemistry V. 47 5608 2008
PubMed-ID: 18442260  |  Reference-DOI: 10.1021/BI800180G

(-) Compounds

Molecule 1 - IMIDAZOLONEPROPIONASE
    Chains: A
    EC Number: 3.5.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1DI61Ligand/Ion3-[(4S)-2,5-DIOXOIMIDAZOLIDIN-4-YL]PROPANOIC ACID
2FE1Ligand/IonFE (III) ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1DI61Ligand/Ion3-[(4S)-2,5-DIOXOIMIDAZOLIDIN-4-YL]PROPANOIC ACID
2FE-1Ligand/IonFE (III) ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 22)
No.NameCountTypeFull Name
1DI62Ligand/Ion3-[(4S)-2,5-DIOXOIMIDAZOLIDIN-4-YL]PROPANOIC ACID
2FE-1Ligand/IonFE (III) ION
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:72 , HIS A:74 , HIS A:242 , ASP A:317 , HOH A:859BINDING SITE FOR RESIDUE FE A 500
2AC2SOFTWAREARG A:81 , TYR A:144 , HIS A:177 , PHE A:214 , HIS A:242 , GLN A:245 , ASN A:319 , GLY A:321 , THR A:322 , HOH A:856 , HOH A:859BINDING SITE FOR RESIDUE DI6 A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q09)

(-) 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 2Q09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q09)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q09)

(-) 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:402
 aligned with HUTI_AERHH | A0KF84 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:404
                                    16        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    
           HUTI_AERHH     7 NCERVWLNVTPATLRSDLADYGLLEPHALGVHEGRIHALVPMQDLKGPYPAHWQDMKGKLVTPGLIDCHTHLIFAGSRAEEFELRQKGVPYAEIARKGGGIISTVRATRAACEEQLFELALPRVKSLIREGVTTVEIKSGYGLTLEDELKMLRVARRLGEALPIRVKTTLLAAHAVPPEYRDDPDSWVETICQEIIPAAAEAGLADAVDVFCEHIGFSLAQTEQVYLAADQYGLAVKGHMDQLSNLGGSTLAANFGALSVDHLEYLDPEGIQALAHRGVVATLLPTAFYFLKETKLPPVAALRKAGVPMAVSSDINPGTAPIVSLRMAMNMACTLFGLTPVEAMAGVTRHAARALGEQEQLGQLRVGMLADFLVWNCGHPAELSYLIGVDQLVSRVINGEETLH 410
               SCOP domains d2q09a1 A:4-65,A:367-407                                      d2q09a2 A:66-366 Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421                                                                                                                                                                                                                              d2q09a1 A:4-65,A:367-407                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------Amidohydro_4-2q09A01 A:58-376                                                                                                                                                                                                                                                                                                  ------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...............eeeeee..eeeeeee.hhh.--.....ee....eeee.eeeeee.......hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhh....eeee.......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
                 2q09 A   4 NCERVWLNVTPATLRSDLADYGLLEPHALGVHEGRIHALVPmQDLK--YPAHWQDmKGKLVTPGLIDCHTHLIFAGSRAEEFELRQKGVPYAEIARKGGGIISTVRATRAASEDQLFELALPRVKSLIREGVTTVEIKSGYGLTLEDELKmLRVARRLGEALPIRVKTTLLAAHAVPPEYRDDPDSWVETICQEIIPAAAEAGLADAVDVFCEHIGFSLAQTEQVYLAADQYGLAVKGHmDQLSNLGGSTLAANFGALSVDHLEYLDPEGIQALAHRGVVATLLPTAFYFLKETKLPPVVALRKAGVPmAVSSDINPGTAPIVSLRmAmNmACTLFGLTPVEAmAGVTRHAARALGEQEQLGQLRVGmLADFLVWNCGHPAELSYLIGVDQLVSRVVNGEETLH 407
                                    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    
                                                                    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)
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  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 2Q09)

(-) 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.

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 Related Entries

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UniProtKB/Swiss-Prot
        HUTI_AERHH | A0KF84: 2oof

(-) Related Entries Specified in the PDB File

2gok CRYSTAL STRUCTURE OF NATIVE IMIDAZOLONEPROPIONASE FROM AGROBACTERIUM TUMEFACIENS. NYSGXRC TARGET 9252B.
2oof CRYSTAL STRUCTURE OF NATIVE 4-IMIDAZOLONE-5-PROPIONATE AMIDOHYDROLASE FROM ENVIRONMENTAL SAMPLE. NYSGXRC TARGET 9252H.
2puz CRYSTAL STRUCTURE OF PRODUCT-BOUND IMIDAZOLONEPROPIONASE FROM AGROBACTERIUM TUMEFACIENS. NYSGXRC TARGET 9252B.