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(-) Description

Title :  THR110ALA DIHYDROOROTASE FROM E. COLI
 
Authors :  M. Lee, M. J. Maher, J. M. Guss
Date :  17 May 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lee, M. J. Maher, R. I. Christopherson, J. M. Guss
Kinetic And Structural Analysis Of Mutant Escherichia Coli Dihydroorotases: A Flexible Loop Stabilizes The Transition State
Biochemistry V. 46 10538 2007
PubMed-ID: 17711307  |  Reference-DOI: 10.1021/BI701098E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    ChainsA, B
    EC Number3.5.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBLUESCRIPT
    Expression System StrainX7014A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYRC
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymDHOASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1DOR2Ligand/Ion(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MLI1Ligand/IonMALONATE ION
4NCD1Ligand/IonN-CARBAMOYL-L-ASPARTATE
5ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:102 , HIS A:139 , HIS A:177 , ZN A:401 , DOR A:1410 , HOH A:1441BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREHIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:400 , HOH A:1441BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWAREKCX B:102 , HIS B:139 , HIS B:177 , ZN B:401 , NCD B:1420 , DOR B:1430 , HOH B:1431BINDING SITE FOR RESIDUE ZN B 400
4AC4SOFTWAREHIS B:16 , HIS B:18 , KCX B:102 , ASP B:250 , ZN B:400 , NCD B:1420 , HOH B:1431BINDING SITE FOR RESIDUE ZN B 401
5AC5SOFTWAREHIS 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:1441 , HOH A:1718 , HOH A:1779BINDING SITE FOR RESIDUE DOR A 1410
6AC6SOFTWAREHIS B:16 , HIS B:18 , ARG B:20 , ASN B:44 , KCX B:102 , HIS B:139 , HIS B:177 , CYS B:221 , LEU B:222 , ASP B:250 , ALA B:252 , HIS B:254 , ALA B:266 , GLY B:267 , ZN B:400 , ZN B:401 , HOH B:1431BINDING SITE FOR RESIDUE NCD B 1420
7AC7SOFTWAREHIS B:18 , ARG B:20 , ASN B:44 , HIS B:139 , CYS B:221 , LEU B:222 , ALA B:252 , HIS B:254 , ALA B:266 , GLY B:267 , ZN B:400 , HOH B:1431BINDING SITE FOR RESIDUE DOR B 1430
8AC8SOFTWAREARG A:207 , ARG A:227 , HOH A:1443 , HOH A:1578 , PHE B:150 , ARG B:207 , ARG B:227 , HOH B:1570 , HOH B:1707BINDING SITE FOR RESIDUE MLI A 1440

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z26)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:46 -Pro A:47
2Leu A:222 -Pro A:223
3Ala B:46 -Pro B:47
4Leu B:222 -Pro B:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z26)

(-) PROSITE Motifs  (2, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2Z26)

(-) 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:344
 aligned with PYRC_ECOLI | P05020 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:344
                                    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    
           PYRC_ECOLI     4 PSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d2z26a_ A: Dihydroorotase                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2z26A00 A:3-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z26 A   3 PSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANATANSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    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    
                                                                                                                             102-KCX                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:335
 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 d2z26b_ B: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2z26B00 B:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -----Amidohydro_1-2z26B01 B:9-322                                                                                                                                                                                                                                                                                              ------------------------ Pfam domains (1)
           Pfam domains (2) -----Amidohydro_1-2z26B02 B:9-322                                                                                                                                                                                                                                                                                              ------------------------ Pfam domains (2)
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhh..eeeeee...--------....hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z26 B   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPA--------GVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    13        23        33        43        53        63        73        83        93       103  |      - |     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      115                                                                                                                                                                                                                                       

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRC_ECOLI | P050201j79 1xge 2e25 2eg6 2eg7 2eg8 2z24 2z25 2z27 2z28 2z29 2z2a 2z2b

(-) Related Entries Specified in the PDB File

1xge WILD-TYPE DIHDYROOROTASE FROM E. COLI
2z24
2z25
2z27
2z28
2z29
2z2a
2z2b