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(-) Description

Title :  THE CRYSTAL STRUCTURE OF DI-ZN DIHYDROPYRIMIDINASE IN COMPLEX WITH HYDANTOIN
 
Authors :  Y. C. Hsieh, M. C. Chen, C. C. Hsu, S. I. Chan, Y. S. Yang
Date :  23 Jun 13  (Deposition) - 18 Sep 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, Zinc Binding, Carboxylation, Alpha-Beta Barrel, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. C. Hsieh, M. C. Chen, C. C. Hsu, S. I. Chan, Y. S. Yang, C. J. Chen
Crystal Structures Of Vertebrate Dihydropyrimidinase And Complexes From Tetraodon Nigroviridis With Lysine Carbamylation: Metal And Structural Requirements For Post-Translational Modification And Function.
J. Biol. Chem. V. 288 30645 2013
PubMed-ID: 24005677  |  Reference-DOI: 10.1074/JBC.M113.496778

(-) Compounds

Molecule 1 - CHROMOSOME 8 SCAF14545, WHOLE GENOME SHOTGUN SEQUENCE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET44A(+)
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPYS, GSTENG00015639001
    Organism Common: SPOTTED GREEN PUFFERFISH
    Organism Scientific: TETRAODON NIGROVIRIDIS
    Organism Taxid: 99883
    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
1HYN1Ligand/IonIMIDAZOLIDINE-2,4-DIONE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1HYN4Ligand/IonIMIDAZOLIDINE-2,4-DIONE
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:155 , HIS A:188 , HIS A:244 , ZN A:602 , HYN A:603BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREHIS A:63 , HIS A:65 , KCX A:155 , ASP A:322 , ZN A:601 , HYN A:603BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWAREPHE A:70 , KCX A:155 , ASP A:322 , ZN A:601 , ZN A:602BINDING SITE FOR RESIDUE HYN A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LCS)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:294 -Pro A:295
2Tyr A:385 -Pro A:386

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LCS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LCS)

(-) Exons   (0, 0)

(no "Exon" information available for 4LCS)

(-) 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    
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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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eee.eeeee..eeeeee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhh.............hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...............eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcs A   4 AGEILIKGGKVVNEDCSFFSDVHIRGGKIVEVGPDLRVPPGARVIDATDRLVIPGGIDTHTHMELAFMGTRAVDDFHIGTKAALAGGTTMILDFVMTQKGQSLLEAYDLWRKTADPKVCCDYSLHVAVTWWSDEVKDEMRTLAQERGVNSFkMFMAYKGLFMLRDDELYAVFSHCKEVGAIAQVHAENGDLIAEGAKKMLSLGITGPEGHELCRPEAVEAEATQRAITIASAVNCPLYVVHVMSKSAADVVSKARKDGRVVFGEPIAASLGTDGTNYWHKDWAHAAQYVMGPPLRPDPSTPGYLMDLLANDDLTLTGTDNCTFSRCQKALGKDDFTRIPNGVNGVEDRMSVIWEKGVHSGKMDENRFVAVTSSNAAKIFNFYPQKGRIAKDSDADVVIWDPKTTRKISAQTHHQAVDYNIFEGMECHGVPVVTVSRGRVVYEEGRLKVSPGQGRFIHRQPFSEFVYKRIRQRDEVGKPAVVIREP 488
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483     
                                                                                                                                                                                 155-KCX
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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  (0, 0)

(no "SCOP Domain" information available for 4LCS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LCS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LCS)

(-) Gene Ontology  (4, 4)

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 Related Entries

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

UniProtKB/TrEMBL
        Q4SMR4_TETNG | Q4SMR4: 4lcq 4lcr

(-) Related Entries Specified in the PDB File

4gz7 4h00 4h01 4lcq 4lcr