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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE CDD-2 (BA4525) FROM BACILLUS ANTHRACIS AT 2.40A RESOLUTION
 
Authors :  V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, O. V. Moroz, A. J. Wilkinson, K. S. Wilson, Structural Proteomics In Europe (S
Date :  21 Sep 05  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Purines, Pyrimidines, Nucleosides, Nucleotides, Salvage Of Nucleosides And Nucleotides, Structural Genomics, Structural Proteomics In Europe, Spine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, O. V. Moroz, A. J. Wilkinson, K. S. Wilson
Crystal Structure Of Cytidine Deaminase Cdd-2 (Ba4525) From Bacillus Anthracis At 2. 40A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CDD-2
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:53 , CYS B:86 , CYS B:89 , HOH B:1037BINDING SITE FOR RESIDUE ZN B 1001
2AC2SOFTWARECYS A:53 , CYS A:86 , CYS A:89 , HOH A:2018BINDING SITE FOR RESIDUE ZN A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D30)

(-) Exons   (0, 0)

(no "Exon" information available for 2D30)

(-) 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:124
 aligned with Q81LT6_BACAN | Q81LT6 from UniProtKB/TrEMBL  Length:132

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
         Q81LT6_BACAN     1 MNSKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGDKEFVAIAIVADTKRPVPPCGACRQVMVELCKQDTKVYLSNLHGDVQETTVGELLPGA 124
               SCOP domains d2d30a1 A:1-124 mono-domain cytidine deaminase                                                                               SCOP domains
               CATH domains 2d30A00 A:1-124 Cytidine Deaminase, domain 2                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhh....eeeee.....eeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d30 A   1 MNSKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGDKEFVAIAIVADTKRPVPPCGACRQVMVELCKQDTKVYLSNLHGDVQETTVGELLPGA 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with Q81LT6_BACAN | Q81LT6 from UniProtKB/TrEMBL  Length:132

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
         Q81LT6_BACAN     1 MNSKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGDKEFVAIAIVADTKRPVPPCGACRQVMVELCKQDTKVYLSNLHGDVQETTVGELLPGA 124
               SCOP domains d2d30b_ B: mono-domain cytidine deaminase                                                                                    SCOP domains
               CATH domains 2d30B00 B:1-124 Cytidine Deaminase, domain 2                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhh....eeeee.....eeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d30 B   1 MNSKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGDKEFVAIAIVADTKRPVPPCGACRQVMVELCKQDTKVYLSNLHGDVQETTVGELLPGA 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D30)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81LT6_BACAN | Q81LT6)
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: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:0009972    cytidine deamination    The removal of amino group in the presence of water.

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