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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A NOVEL, LATENT DIHYDROOROTASE FROM AQUIFEX AEOLICUS AT 1.7 A RESOLUTION
 
Authors :  P. D. Martin, C. Purcarea, P. Zhang, A. Vaishnav, S. Sadecki, H. I. Guy-E D. R. Evans, B. F. Edwards
Date :  14 Oct 04  (Deposition) - 05 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Dihydroorotase, Amidohydrolase, Metalloenzyme, Pyrimidine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Martin, C. Purcarea, P. Zhang, A. Vaishnav, S. Sadecki, H. I. Guy-Evans, D. R. Evans, B. F. Edwards
The Crystal Structure Of A Novel, Latent Dihydroorotase Fro Aquifex Aeolicus At 1. 7A Resolution
J. Mol. Biol. V. 348 535 2005
PubMed-ID: 15826652  |  Reference-DOI: 10.1016/J.JMB.2005.03.015

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A
    EC Number: 3.5.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRC
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: DHOASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:61 , HIS A:63 , ASP A:153 , ASP A:305 , HOH A:1425BINDING SITE FOR RESIDUE ZN A 1423
2AC2SOFTWARELYS A:72 , HIS A:309 , GLN A:310 , THR A:311 , HOH A:1564 , HOH A:1612 , HOH A:1731BINDING SITE FOR RESIDUE SO4 A 1424

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:66 -Pro A:67
2Asn A:97 -Pro A:98
3Met A:321 -Pro A:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XRF)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYRC_AQUAE59-67  1A:59-67
2DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYRC_AQUAE303-314  1A:303-311

(-) Exons   (0, 0)

(no "Exon" information available for 1XRF)

(-) 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:363
 aligned with PYRC_AQUAE | O66990 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:423
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419   
           PYRC_AQUAE     - -MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
               SCOP domains -d1xrfa1 A:1-55,A:366-422 Two-domain dihydroorotase     d1xrfa2 A:56-365 Two-domain dihydroorotase                                                                                                                                                                                                                                                                            d1xrfa1 A:1-55,A:366-422 Two-domain dihydroorotase        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------Amidohydro_4-1xrfA01 A:47-376                                                                                                                                                                                                                                                                                                             ---------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeehhhheeee.eeeee..eeeeee.......eeeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee....hhhhh.....hhhhhhhhh............hhhhhhhhhhhhhhhh..eee.----------------------------hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeehhhhhh-----------------------hhhhhhhhhhh....ee.........---------.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............eeeeeeeeeee..................eeeeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------DIHYDROOR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xrf A   0 WMLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDH----------------------------AEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLL-----------------------DRLALIEGVKRGIIDCFATDHAPHQT---------MPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179|        -         -       209       219       229       239       249       259  |      -         -      |289       299       309 |       - |     329       339       349       359       369       379       389       399       409       419   
                                                                                                                                                                                                              180                          209                                                  262                     286                      311       321
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XRF)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYRC_AQUAE | O66990)
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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRC_AQUAE | O66990: 1xrt 3d6n 4bjh

(-) Related Entries Specified in the PDB File

1xrt