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(-) Description

Title :  MOLECULAR STRUCTURE OF DIHYDROOROTASE: A PARADIGM FOR CATALYSIS THROUGH THE USE OF A BINUCLEAR METAL CENTER
 
Authors :  J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden
Date :  16 May 01  (Deposition) - 20 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Metalloenzyme, Pyrimidine Biosynthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden
Molecular Structure Of Dihydroorotase: A Paradigm For Catalysis Through The Use Of A Binuclear Metal Center.
Biochemistry V. 40 6989 2001
PubMed-ID: 11401542  |  Reference-DOI: 10.1021/BI010682I
(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 Taxid562
    GenePYRC
    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  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NCD2Ligand/IonN-CARBAMOYL-L-ASPARTATE
3ORO1Ligand/IonOROTIC ACID
4ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:401 , HOH A:1407BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREKCX A:102 , HIS A:139 , HIS A:177 , ZN A:400 , ORO A:410 , HOH A:1407BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWAREHIS B:16 , HIS B:18 , KCX B:102 , ASP B:250 , NCD B:411BINDING SITE FOR RESIDUE ZN B 400
4AC4SOFTWAREKCX B:102 , HIS B:139 , HIS B:177 , NCD B:411BINDING SITE FOR RESIDUE ZN B 401
5AC5SOFTWAREHIS A:18 , ARG A:20 , ASN A:44 , HIS A:139 , CYS A:221 , LEU A:222 , ASP A:250 , ALA A:252 , HIS A:254 , ALA A:266 , GLY A:267 , ZN A:401 , HOH A:1160 , HOH A:1407BINDING SITE FOR RESIDUE ORO A 410
6AC6SOFTWAREHIS B:18 , ARG B:20 , ASN B:44 , KCX B:102 , HIS B:139 , 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:1485BINDING SITE FOR RESIDUE NCD B 411
7AC7SOFTWAREASN A:208 , HIS A:209 , VAL A:212 , HOH A:1110 , HOH A:1446 , ALA B:145 , ARG B:152BINDING SITE FOR RESIDUE NCD A 950

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J79)

(-) 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 1J79)

(-) 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 1J79)

(-) 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: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 d1j79a_ A: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j79A00 A:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhh..eee..................hhhhhhhhhhhhhhh..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
                 1j79 A   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAPHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFQRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 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                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:339
 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 d1j79b_ B: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j79B00 B:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhh..eee........----.....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j79 B   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAPHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANA----SHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFQRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 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-KCX08  113                                                                                                                                                                                                                                         

   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  (0, 0)

(no "Pfam Domain" information available for 1J79)

(-) 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 | P050201xge 2e25 2eg6 2eg7 2eg8 2z24 2z25 2z26 2z27 2z28 2z29 2z2a 2z2b

(-) Related Entries Specified in the PDB File

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