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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROOROTASE FROM THERMUS THERMOPHILUS
 
Authors :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Zinc Binding Protein, Hydrolase, Metal-Binding, Pyrimidine Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Dihydroorotase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A
    EC Number: 3.5.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:147 , ASP A:306 , ZN A:1006BINDING SITE FOR RESIDUE ZN A 1004
2AC2SOFTWAREASP A:147 , HIS A:174 , HIS A:233 , ZN A:1004BINDING SITE FOR RESIDUE ZN A 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z00)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:17 -Pro A:18
2Glu A:60 -Pro A:61
3Lys A:91 -Pro A:92
4Ala A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z00)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z00)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z00)

(-) 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:426
 aligned with Q5SK67_THET8 | Q5SK67 from UniProtKB/TrEMBL  Length:426

    Alignment length:426
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420      
         Q5SK67_THET8     1 MILIRNVRLVDARGERGPADVLIGEGRILSLEGGEAKQVVDGTGCFLAPGFLDLHAHLREPGEEVKEDLFSGLLAAVRGGYTDLVSMPNTKPPVDTPEAVRALKEKAKALGLARLHPAAALTEKQEGKTLTPAGLLREAGAVLLTDDGRTNEDAGVLAAGLLMAAPLGLPVAVHAEDAGLRRNGVMNDGPLADLLGLPGNPPEAEAARIARDLEVLRYALRRSPATPRLHVQHLSTKRGLELVREAKRAGLPVTAEATPHHLTLTEEALRTFDPLFKVAPPLRGEEDREALLEGLLDGTLDAIATDHAPHTLAEKEKDLLRAPFGIPSLEVAFPLLYTELHLKRGFPLQRLVELFTDGPRRVLGLPPLHLEEGAEASLVLLSPKERPVDPSAFASKARYSPWAGWVLGGWPVLTLVAGRIVHEALK 426
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------Amidohydro_4-2z00A01 A:41-379                                                                                                                                                                                                                                                                                                                      ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeeeeeee..eeee.......eeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..ee..ee..hhhhh.....hhhhhhhhh..eee.......hhhhhhhhhhhhhhhh..eee...hhhhhh...ee.hhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh....ee.........hhhhh.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eeeee...ee.hhhhh............ee..eeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z00 A   1 mILIRNVRLVDARGERGPADVLIGEGRILSLEGGEAKQVVDGTGCFLAPGFLDLHAHLREPGEEVKEDLFSGLLAAVRGGYTDLVSmPNTKPPVDTPEAVRALKEKAKALGLARLHPAAALTEKQEGKTLTPAGLLREAGAVLLTDDGRTNEDAGVLAAGLLmAAPLGLPVAVHAEDAGLRRNGVmNDGPLADLLGLPGNPPEAEAARIARDLEVLRYALRRSPATPRLHVQHLSTKRGLELVREAKRAGLPVTAEATPHHLTLTEEALRTFDPLFKVAPPLRGEEDREALLEGLLDGTLDAIATDHAPHTLAEKEKDLLRAPFGIPSLEVAFPLLYTELHLKRGFPLQRLVELFTDGPRRVLGLPPLHLEEGAEASLVLLSPKERPVDPSAFASKARYSPWAGWVLGGWPVLTLVAGRIVHEALK 426
                            |       10        20        30        40        50        60        70        80      | 90       100       110       120       130       140       150       160  |    170       180     | 190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420      
                            |                                                                                    87-MSE                                                                     163-MSE                186-MSE                                                                                                                                                                                                                                            
                            1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2Z00)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z00)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SK67_THET8 | Q5SK67)
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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