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(-) Description

Title :  YEAST CYTOSINE DEAMINASE DOUBLE MUTANT
 
Authors :  A. Korkegian, M. E. Black, D. Baker, B. L. Stoddard
Date :  08 Feb 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Cytosine Deaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Korkegian, M. E. Black, D. Baker, B. L. Stoddard
Computational Thermostabilization Of An Enzyme.
Science V. 308 857 2005
PubMed-ID: 15879217  |  Reference-DOI: 10.1126/SCIENCE.1107387
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOSINE DEAMINASE
    ChainsA, B
    EC Number3.5.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFCY1
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymCYTOSINE AMINOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:64 , ZN A:501 , HOH A:1128 , HOH A:1129 , HOH A:1132 , HOH A:1133BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:62 , CYS A:91 , CYS A:94 , ZN A:500 , HOH A:1133BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWAREHIS B:262 , CYS B:291 , CYS B:294 , ZN B:503 , HOH B:1131BINDING SITE FOR RESIDUE ZN B 502
4AC4SOFTWAREGLU B:264 , ZN B:502 , HOH B:1130 , HOH B:1131 , HOH B:1134 , HOH B:1135BINDING SITE FOR RESIDUE ZN B 503
5AC5SOFTWAREGLY B:326 , ASP B:346 , HOH B:1064 , HOH B:1090 , HOH B:1136BINDING SITE FOR RESIDUE CA B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YSD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.FCY1_YEAST9-129
 
  2A:9-129
B:209-329
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.FCY1_YEAST62-98
 
  2A:62-98
B:262-298

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR062W1YPR062W.1XVI:677162-677638477FCY1_YEAST1-1581582A:3-158
B:201-358
156
158

(-) 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:156
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           FCY1_YEAST     3 TGGMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d1ysda1 A:3-158 Cytosine deaminase                                                                                                                           SCOP domains
               CATH domains 1ysdA00 A:3-158 Cytidine Deaminase, domain 2                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeeeee..hhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------CYT_DCMP_DEAMINASES_2  PDB: A:9-129 UniProt: 9-129                                                                       ----------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:62-98  ------------------------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:3-158 UniProt: 1-158 [INCOMPLETE]                                                                                                           Transcript 1
                 1ysd A   3 TGGMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 158
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:161
                               1                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 
           FCY1_YEAST     - ---MVTGGMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d1ysdb_ B: Cytosine deaminase                                                                                                                                     SCOP domains
               CATH domains 1ysdB00 B:198-358 Cytidine Deaminase, domain 2                                                                                                                    CATH domains
           Pfam domains (1) ----------dCMP_cyt_deam_1-1ysdB01 B:208-310                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------dCMP_cyt_deam_1-1ysdB02 B:208-310                                                                      ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeee....hhhhhhhhhhhh..eeee........hhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------CYT_DCMP_DEAMINASES_2  PDB: B:209-329 UniProt: 9-129                                                                     ----------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:262-298------------------------------------------------------------ PROSITE (2)
               Transcript 1 ---Exon 1.1  PDB: B:201-358 UniProt: 1-158                                                                                                                        Transcript 1
                 1ysd B 198 GSSMVTGGMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 358
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357 

   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CDA (39)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FCY1_YEAST | Q12178)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004131    cytosine deaminase activity    Catalysis of the reaction: cytosine + H2O = uracil + NH3.
    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: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:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0044206    UMP salvage    Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
    GO:0046087    cytidine metabolic process    The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside.
    GO:0019858    cytosine metabolic process    The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.
    GO:0008655    pyrimidine-containing compound salvage    Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FCY1_YEAST | Q121781ox7 1p6o 1rb7 1uaq 1ysb 2o3k

(-) Related Entries Specified in the PDB File

1ysb