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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROPYRIMIDINASE FROM DICTYOSTELIUM DISCOIDEUM
 
Authors :  B. Lohkamp, D. Dobritzsch
Date :  25 Jan 06  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  (Beta-Alpha)8-Barrel, Beta-Sandwich, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Lohkamp, B. Andersen, J. Piskur, D. Dobritzsch
The Crystal Structures Of Dihydropyrimidinases Reaffirm The Close Relationship Between Cyclic Amidohydrolases And Explain Their Substrate Specificity.
J. Biol. Chem. V. 281 13762 2006
PubMed-ID: 16517602  |  Reference-DOI: 10.1074/JBC.M513266200

(-) Compounds

Molecule 1 - DIHYDROPYRIMIDINE AMIDOHYDROLASE
    Chains: A
    EC Number: 3.5.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: P343
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PYD2
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689
    Synonym: DIHYDROPYRIMIDINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2MLI1Ligand/IonMALONATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2MLI4Ligand/IonMALONATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , HIS A:68 , KCX A:158 , ASP A:325 , HOH A:762BINDING SITE FOR RESIDUE ZN A 522
2AC2SOFTWAREKCX A:158 , HIS A:191 , HIS A:247BINDING SITE FOR RESIDUE ZN A 523
3AC3SOFTWARETYR A:23 , TRP A:370 , ASP A:472 , GLY A:473 , HOH A:797BINDING SITE FOR RESIDUE MLI A 524

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:297 -Pro A:298
2Tyr A:388 -Pro A:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FTW)

(-) 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:484
 aligned with DPYS_DICDI | Q55DL0 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:484
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    
           DPYS_DICDI     7 TGTILIKNGTVVNDDRYFKSDVLVENGIIKEISKNIEPKEGIKVVDATDKLLLPGGIDTHTHFQLPFMGTVSVDDFDIGTQAAVAGGTTFIIDFVIPTRGQSLLEAYDQWKKWADEKVNCDYSLHVAITWWSEQVSREMEILVKERGVNSFKCFMAYKNSFMVTDQEMYHIFKRCKELGAIAQVHAENGDMVFEGQKKMLEMGITGPEGHELSRPEALEAEATNRAIVIADSVCTPVYIVHVQSIGAADVICKHRKEGVRVYGEPIAAGLGVDGSHMWNHDWRHAAAFVMGPPIRPDPRTKGVLMDYLARGDLDCVGTDNCTFCADQKAMGKDDFTKIPNGVNGVEDRMSIVWENGVNTGKLTWCQFVRATSSEAARIFNIYPRKGRIDVGCDGDIVIWDPNQSKTISKDTHHHAVDFNIFEGIKVTGIAVTTIVAGNIVWSDNKLSCVKGSGRFVPRPPFGPVFDGIEQRDKVRNELLRKVDR 490
               SCOP domains d2ftwa1 A:7-59,A:394-490                             d2ftwa2 A:60-393 Dihydropyrimidine amidohydrolase Pyd2                                                                                                                                                                                                                                                                                        d2ftwa1 A:7-59,A:394-490 Dihydropyrimidine amidohydrolase Pyd2                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee....eee.eeeee..eeeeee..........eee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh.hhhhhhh...........hhhhhhhhhhhh.............hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ftw A   7 TGTILIKNGTVVNDDRYFKSDVLVENGIIKEISKNIEPKEGIKVVDATDKLLLPGGIDTHTHFQLPFMGTVSVDDFDIGTQAAVAGGTTFIIDFVIPTRGQSLLEAYDQWKKWADEKVNCDYSLHVAITWWSEQVSREMEILVKERGVNSFkCFMAYKNSFMVTDQEMYHIFKRCKELGAIAQVHAENGDMVFEGQKKMLEMGITGPEGHELSRPEALEAEATNRAIVIADSVCTPVYIVHVQSIGAADVICKHRKEGVRVYGEPIAAGLGVDGSHMWNHDWRHAAAFVMGPPIRPDPRTKGVLMDYLARGDLDCVGTDNCTFCADQKAMGKDDFTKIPNGVNGVEDRMSIVWENGVNTGKLTWCQFVRATSSERARIFNIYPRKGRIDVGCDGDIVIWDPNQSKTISKDTHHHAVDFNIFEGIKVTGIAVTTIVAGNIVWSDNKLSCVKGSGRFVPRPPFGPVFDGIEQRDKVRNELLRKVDR 490
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156 |     166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    
                                                                                                                                                                                 158-KCX
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FTW)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (DPYS_DICDI | Q55DL0)
molecular function
    GO:0004157    dihydropyrimidinase activity    Catalysis of the reaction: 5,6-dihydrouracil + H2O = 3-ureidopropionate.
    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: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:0006208    pyrimidine nucleobase catabolic process    The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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