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(-) Description

Title :  YEAST CYTOSINE DEAMINASE D92E TRIPLE MUTANT BOUND TO TRANSITION STATE ANALOGUE HPY
 
Authors :  A. M. Korkegian, B. L. Stoddard
Date :  01 Dec 06  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Transition State Analogue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Stolworthy, A. M. Korkegian, C. Willmon, B. L. Stoddard, M. E. Black
Crystal Structure Of Yeast Cytosine Deaminase D92E Triple Mutant Bound To Transition State Analogue Hpy
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOSINE DEAMINASE
    ChainsA, B
    EC Number3.5.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2HPY2Ligand/Ion4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:262 , CYS B:291 , CYS B:294 , HPY B:410BINDING SITE FOR RESIDUE ZN B 400
2AC2SOFTWAREHIS A:62 , CYS A:91 , CYS A:94 , HPY A:411BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWAREGLU A:128 , GLN A:150 , HOH A:423 , HOH A:435 , GLU B:275BINDING SITE FOR RESIDUE CA B 403
4AC4SOFTWAREILE B:233 , ASN B:251 , HIS B:262 , GLY B:263 , GLU B:264 , CYS B:291 , CYS B:294 , ASP B:355 , ZN B:400BINDING SITE FOR RESIDUE HPY B 410
5AC5SOFTWAREILE A:33 , ASN A:51 , HIS A:62 , GLY A:63 , GLU A:64 , PRO A:90 , CYS A:91 , CYS A:94 , ASP A:155 , ZN A:401BINDING SITE FOR RESIDUE HPY A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O3K)

(-) 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:5-158
B:206-358
154
153

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:154
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    
           FCY1_YEAST     5 GMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d2o3ka_ A: Cytosine deaminase                                                                                                                              SCOP domains
               CATH domains 2o3kA00 A:5-158 Cytidine Deaminase, domain 2                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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: 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:5-158 UniProt: 1-158 [INCOMPLETE]                                                                                                         Transcript 1
                 2o3k A   5 GMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCEMCTGAIIMYGIPRCVIGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:153
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155   
           FCY1_YEAST     6 MASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d2o3kb_ B: Cytosine deaminase                                                                                                                             SCOP domains
               CATH domains 2o3kB00 B:206-358 Cytidine Deaminase, domain 2                                                                                                            CATH domains
           Pfam domains (1) --dCMP_cyt_deam_1-2o3kB01 B:208-310                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --dCMP_cyt_deam_1-2o3kB02 B:208-310                                                                      ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeeeee..hhhhhhhhhhh...eeeeee......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:206-358 UniProt: 1-158 [INCOMPLETE]                                                                                                      Transcript 1
                 2o3k B 206 MASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCEMCTGAIIMYGIPRCVIGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 358
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355   

   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  (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 1ysd

(-) Related Entries Specified in the PDB File

1ysb CRYSTAL STRUCTURE OF YEAST CYTOSINE DEAMINASE TRIPLE MUTANT (A23L,V108I,I140L)