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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE CDD1, AN ORPHAN C TO U EDITASE FROM YEAST
 
Authors :  K. Xie, M. P. Sowden, G. S. C. Dance, A. T. Torelli, H. C. Smith, J. E. Wedekind
Date :  13 Oct 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Zinc Dependent Deaminase, Rna Editing, Apobec-1 Related Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xie, M. P. Sowden, G. S. Dance, A. T. Torelli, H. C. Smith, J. E. Wedekind
The Structure Of A Yeast Rna-Editing Deaminase Provides Insight Into The Fold And Function Of Activation-Induced Deaminase And Apobec-1.
Proc. Natl. Acad. Sci. Usa V. 101 8114 2004
PubMed-ID: 15148397  |  Reference-DOI: 10.1073/PNAS.0400493101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE
    Chains: A, B, C, D
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) CODONPLUS(TM)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDD1P
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CYTIDINE AMINOHYDROLASE, CDA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:61 , CYS A:96 , CYS A:99 , HOH A:223BINDING SITE FOR RESIDUE ZN A 150
2AC2SOFTWARECYS B:61 , CYS B:96 , CYS B:99 , HOH B:209BINDING SITE FOR RESIDUE ZN B 151
3AC3SOFTWARECYS C:61 , CYS C:96 , CYS C:99 , HOH C:198BINDING SITE FOR RESIDUE ZN C 152
4AC4SOFTWARECYS D:61 , CYS D:96 , CYS D:99 , HOH D:179BINDING SITE FOR RESIDUE ZN D 153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R5T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R5T)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.CDD_YEAST9-139
 
 
 		  4A:9-139
B:9-139
C:9-139
D:9-136
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.CDD_YEAST61-103
 
 
 		  4A:61-103
B:61-103
C:61-103
D:61-103

(-) Exons   (1, 4)

Asymmetric/Biological Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR245C1YLR245C.1XII:626932-626504429CDD_YEAST1-1421424A:2-142
B:1-139
C:2-141
D:3-136		141
139
140
134

(-) 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:141
 aligned with CDD_YEAST | Q06549 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            CDD_YEAST     2 KVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHLN 142
               SCOP domains d1r5ta_ A: mono-domain cytidine deaminase                                                                                                     SCOP domains
               CATH domains 1r5tA00 A:2-142 Cytidine Deaminase, domain 2                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh........eeeeee.....eeeee.....hhhhh.hhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhh......eeeee......eeeeehhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------CYT_DCMP_DEAMINASES_2  PDB: A:9-139 UniProt: 9-139                                                                                 --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:61-103       --------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-142 UniProt: 1-142 [INCOMPLETE]                                                                                            Transcript 1
                 1r5t A   2 KVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHLN 142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with CDD_YEAST | Q06549 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
            CDD_YEAST     1 MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPS 139
               SCOP domains d1r5tb_ B: mono-domain cytidine deaminase                                                                                                   SCOP domains
               CATH domains 1r5tB00 B:1-139 Cytidine Deaminase, domain 2                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh........eeeeee.....eeeee.....hhhhh.hhhhhhhhhhhhh.......eeeeee.........hhhhhhhhh.......eeeee......eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------CYT_DCMP_DEAMINASES_2  PDB: B:9-139 UniProt: 9-139                                                                                  PROSITE (1)
                PROSITE (2) ------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:61-103       ------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:1-139 UniProt: 1-142 [INCOMPLETE]                                                                                          Transcript 1
                 1r5t B   1 MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPS 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain C from PDB  Type:PROTEIN  Length:140
 aligned with CDD_YEAST | Q06549 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
            CDD_YEAST     2 KVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHL 141
               SCOP domains d1r5tc_ C: mono-domain cytidine deaminase                                                                                                    SCOP domains
               CATH domains 1r5tC00 C:2-141 Cytidine Deaminase, domain 2                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh........eeeeee.....eeeee.....hhhhh.hhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhh......eeeee......eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------CYT_DCMP_DEAMINASES_2  PDB: C:9-139 UniProt: 9-139                                                                                 -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:61-103       -------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:2-141 UniProt: 1-142 [INCOMPLETE]                                                                                           Transcript 1
                 1r5t C   2 KVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHL 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with CDD_YEAST | Q06549 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:134
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    
            CDD_YEAST     3 VGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAF 136
               SCOP domains d1r5td_ D: mono-domain cytidine deaminase                                                                                              SCOP domains
               CATH domains 1r5tD00 D:3-136 Cytidine Deaminase, domain 2                                                                                           CATH domains
           Pfam domains (1) -----dCMP_cyt_deam_1-1r5tD01 D:8-115                                                                             --------------------- Pfam domains (1)
           Pfam domains (2) -----dCMP_cyt_deam_1-1r5tD02 D:8-115                                                                             --------------------- Pfam domains (2)
           Pfam domains (3) -----dCMP_cyt_deam_1-1r5tD03 D:8-115                                                                             --------------------- Pfam domains (3)
           Pfam domains (4) -----dCMP_cyt_deam_1-1r5tD04 D:8-115                                                                             --------------------- Pfam domains (4)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.........eeeee.....eeeee.....hhhhh.hhhhhhhhhhhhh.......eeeee..........hhhhhhhhhh......eeeee......eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------CYT_DCMP_DEAMINASES_2  PDB: D:9-136 UniProt: 9-139                                                                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:61-103       --------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:3-136 UniProt: 1-142 [INCOMPLETE]                                                                                     Transcript 1
                 1r5t D   3 VGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAF 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CDD_YEAST | Q06549)
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:0004126    cytidine deaminase activity    Catalysis of the reaction: cytidine + H2O = uridine + 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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006216    cytidine catabolic process    The chemical reactions and pathways resulting in the breakdown of cytidine, cytosine riboside, a widely distributed nucleoside.
    GO:0009972    cytidine deamination    The removal of amino group in the presence of water.
    GO:0006217    deoxycytidine catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  1r5t
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 Related Entries

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(-) Related Entries Specified in the PDB File

1af2 DIMERIC CRYSTAL STRUCTURE OF BACTERIAL CYTIDINE DEAMINASE COMPLEXED WITH URIDINE
1jtk TETRAMERIC CRYSTAL STRUCTURE OF BACTERIAL CYTIDINE DEAMINASE FROM BACILLUS SUBTILIS IN COMPLEX WITH THE INHIBITOR TETRAHYDRODEOXYURIDINE