Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  2.4 ANGSTROM CRYSTAL STRUCTURE OF DIHYDROOROTASE (PYRC) FROM CAMPYLOBACTER JEJUNI.
 
Authors :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papa W. F. Anderson, Center For Structural Genomics Of Infectious (Csgid)
Date :  19 Nov 10  (Deposition) - 01 Dec 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Dihydroorotase, Zinc Binding, Hydrolase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 4 Angstrom Crystal Structure Of Dihydroorotase (Pyrc) Fro Campylobacter Jejuni.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A, B
    EC Number: 3.5.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: KRX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CJ0259, PYRC
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2PO42Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:92 , HIS A:131 , HIS A:165 , ZN A:337 , HOH A:447BINDING SITE FOR RESIDUE ZN A 336
2AC2SOFTWAREHIS A:10 , HIS A:12 , KCX A:92 , ASP A:237 , ZN A:336 , HOH A:447BINDING SITE FOR RESIDUE ZN A 337
3AC3SOFTWAREGLU A:78 , TYR A:82BINDING SITE FOR RESIDUE PO4 A 338
4AC4SOFTWAREKCX B:92 , HIS B:131 , HIS B:165 , ZN B:337 , HOH B:466BINDING SITE FOR RESIDUE ZN B 336
5AC5SOFTWAREHIS B:10 , HIS B:12 , KCX B:92 , ASP B:237 , ZN B:336 , HOH B:466BINDING SITE FOR RESIDUE ZN B 337
6AC6SOFTWAREGLU B:78 , TYR B:82BINDING SITE FOR RESIDUE PO4 B 338

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PNU)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ile A:40 -Pro A:41
2Lys A:209 -Pro A:210
3Gly A:250 -Cys A:251
4Ile B:40 -Pro B:41
5Glu B:63 -Asn B:64
6Lys B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PNU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PNU)

(-) Exons   (0, 0)

(no "Exon" information available for 3PNU)

(-) 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:338
 aligned with Q0PBP6_CAMJE | Q0PBP6 from UniProtKB/TrEMBL  Length:335

    Alignment length:344
                                     1                                                                                                                                                                                                                                                                                                                                              
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331    
         Q0PBP6_CAMJE     - ---------MKLKNPLDMHLHLRDNQMLELIAPLSARDFCAAVIMPNLIPPLCNLEDLKAYKMRILKACKDENFTPLMTLFFKNYDEKFLYSAKDEIFGIKLYPAGITTNSNGGVSSFDIEYLKPTLEAMSDLNIPLLVHGETNDFVMDRESNFAKIYEKLAKHFPRLKIVMEHITTKTLCELLKDYENLYATITLHHLIITLDDVIGGKMNPHLFCKPIAKRYEDKEALCELAFSGYEKVMFGSDSAPHPKDTKECCGCAAGVFSAPVILPVLAELFKQNSSEENLQKFLSDNTCKIYDLKFKEDKILTLEEKEWQVPNVYEDKYNQVVPYMAGEILKFQLKH 335
               SCOP domains d3pnua_ A: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eeeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhh....eeee................hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh..eeeee.hhhhh.hhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.........------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...ee....ee....ee.......ee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnu A  -8 ENLYFQSNAMKLKNPLDMHLHLRDNQMLELIAPLSARDFCAAVIMPNLIPPLCNLEDLKAYKMRILKACKDENFTPLMTLFFKNYDEKFLYSAKDEIFGIkLYPAGITTNSNGGVSSFDIEYLKPTLEAMSDLNIPLLVHGETNDFVMDRESNFAKIYEKLAKHFPRLKIVMEHITTKTLCELLKDYENLYATITLHHLIITLDDVIGGKMNPHLFCKPIAKRYEDKEALCELAFSGYEKVMFGSDSAPHPK------GCAAGVFSAPVILPVLAELFKQNSSEENLQKFLSDNTCKIYDLKFKEDKILTLEEKEWQVPNVYEDKYNQVVPYMAGEILKFQLKH 335
                                     1        11        21        31        41        51        61        71        81        91|      101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 |     251       261       271       281       291       301       311       321       331    
                                                                                                                               92-KCX                                                                                                                                                243    250                                                                                     


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with Q0PBP6_CAMJE | Q0PBP6 from UniProtKB/TrEMBL  Length:335

    Alignment length:344
                                     1                                                                                                                                                                                                                                                                                                                                              
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331    
         Q0PBP6_CAMJE     - ---------MKLKNPLDMHLHLRDNQMLELIAPLSARDFCAAVIMPNLIPPLCNLEDLKAYKMRILKACKDENFTPLMTLFFKNYDEKFLYSAKDEIFGIKLYPAGITTNSNGGVSSFDIEYLKPTLEAMSDLNIPLLVHGETNDFVMDRESNFAKIYEKLAKHFPRLKIVMEHITTKTLCELLKDYENLYATITLHHLIITLDDVIGGKMNPHLFCKPIAKRYEDKEALCELAFSGYEKVMFGSDSAPHPKDTKECCGCAAGVFSAPVILPVLAELFKQNSSEENLQKFLSDNTCKIYDLKFKEDKILTLEEKEWQVPNVYEDKYNQVVPYMAGEILKFQLKH 335
               SCOP domains d3pnub_ B: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eeeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhh....eeee........-----.......hhhhhhhhhhh...eee...........hhhhhhhhhhhhhhh....eee....hhhhhhhhh....eeeee.hhhhh.hhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee..........-----.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee....ee....ee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnu B  -8 ENLYFQSNAMKLKNPLDMHLHLRDNQMLELIAPLSARDFCAAVIMPNLIPPLCNLEDLKAYKMRILKACKDENFTPLMTLFFKNYDEKFLYSAKDEIFGIkLYPAGITTN-----SSFDIEYLKPTLEAMSDLNIPLLVHGETNDFVMDRESNFAKIYEKLAKHFPRLKIVMEHITTKTLCELLKDYENLYATITLHHLIITLDDVIGGKMNPHLFCKPIAKRYEDKEALCELAFSGYEKVMFGSDSAPHPKD-----GCAAGVFSAPVILPVLAELFKQNSSEENLQKFLSDNTCKIYDLKFKEDKILTLEEKEWQVPNVYEDKYNQVVPYMAGEILKFQLKH 335
                                     1        11        21        31        41        51        61        71        81        91|      101     | 111       121       131       141       151       161       171       181       191       201       211       221       231       241  |    251       261       271       281       291       301       311       321       331    
                                                                                                                               92-KCX  101   107                                                                                                                                      244   250
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PNU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PNU)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q0PBP6_CAMJE | Q0PBP6)
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.
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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:63 - Asn B:64   [ RasMol ]  
    Gly A:250 - Cys A:251   [ RasMol ]  
    Ile A:40 - Pro A:41   [ RasMol ]  
    Ile B:40 - Pro B:41   [ RasMol ]  
    Lys A:209 - Pro A:210   [ RasMol ]  
    Lys B:209 - Pro B:210   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3pnu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q0PBP6_CAMJE | Q0PBP6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.2.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q0PBP6_CAMJE | Q0PBP6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PNU)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PNU)