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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE T109S MUTANT OF E. COLI DIHYDROOROTASE COMPLEXED WITH AN INHIBITOR 5-FLUOROOROTATE
 
Authors :  M. Lee, M. J. Maher, J. M. Guss
Date :  08 Nov 06  (Deposition) - 13 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lee, M. J. Maher, J. M. Guss
Structure Of The T109S Mutant Of Escherichia Coli Dihydroorotase Complexed With The Inhibitor 5-Fluoroorotate Catalytic Activity Is Reflected By The Crystal Form
Acta Crystallogr. , Sect. F V. 63 154 2007
PubMed-ID: 17329804  |  Reference-DOI: 10.1107/S1744309107004009

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A
    EC Number: 3.5.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBLUESCRIPT
    Expression System Strain: X7014A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PYRC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DHOASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1FOT1Ligand/Ion5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FOT2Ligand/Ion5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:102 , HIS A:139 , HIS A:177 , ZN A:401 , FOT A:410 , HOH A:420BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREHIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:400 , HOH A:420BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWAREHIS A:18 , ARG A:20 , ASN A:44 , HIS A:139 , CYS A:221 , LEU A:222 , ALA A:252 , HIS A:254 , ALA A:266 , GLY A:267 , ZN A:400 , HOH A:420BINDING SITE FOR RESIDUE FOT A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E25)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:46 -Pro A:47
2Leu A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E25)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYRC_ECOLI15-23  1A:14-22
2DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYRC_ECOLI249-260  1A:248-259
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYRC_ECOLI15-23  2A:14-22
2DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYRC_ECOLI249-260  2A:248-259

(-) Exons   (0, 0)

(no "Exon" information available for 2E25)

(-) 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:343
 aligned with PYRC_ECOLI | P05020 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:343
                                    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   
           PYRC_ECOLI     5 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d2e25a_ A: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2e25A00 A:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhh..eeeeee..................hhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhh...eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e25 A   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANASTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    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   
                                                                                                                            102-KCX
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  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E25)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRC_ECOLI | P05020)
molecular function
    GO:0004151    dihydroorotase activity    Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
    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: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: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:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0019856    pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2e25
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  PYRC_ECOLI | P05020
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRC_ECOLI | P05020: 1j79 1xge 2eg6 2eg7 2eg8 2z24 2z25 2z26 2z27 2z28 2z29 2z2a 2z2b

(-) Related Entries Specified in the PDB File

1xge WILD-TYPE PROTEIN COMPLEXED WITH L-DHO