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(-) Description

Title :  BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56 - GLN SUBSTITUTION
 
Authors :  E. Johansson, J. Neuhard, M. Willemoes, S. Larsen
Date :  18 Feb 04  (Deposition) - 20 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Cytidine Deaminase, Cdd, Tetramer, Zinc Binding, Pyrimidine Metabolism, Salvage, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Johansson, J. Neuhard, M. Willemoes, S. Larsen
Structural, Kinetic, And Mutational Studies Of The Zinc Ion Environment In Tetrameric Cytidine Deaminase
Biochemistry V. 43 6020 2004
PubMed-ID: 15147186  |  Reference-DOI: 10.1021/BI035893X

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCR56QCDA
    Expression System Strain: JF611
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: CYTIDINE AMINOHYDROLASE, CDA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1THU2Ligand/IonTETRAHYDRODEOXYURIDINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1THU4Ligand/IonTETRAHYDRODEOXYURIDINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:53 , CYS A:86 , CYS A:89 , THU A:138BINDING SITE FOR RESIDUE ZN A1131
2AC2SOFTWARECYS B:53 , CYS B:86 , CYS B:89 , THU B:138BINDING SITE FOR RESIDUE ZN B1131
3AC3SOFTWAREPHE A:24 , VAL A:26 , ASN A:42 , GLU A:44 , CYS A:53 , ALA A:54 , GLU A:55 , PRO A:85 , CYS A:86 , CYS A:89 , ZN A:1131 , ALA B:46 , ALA B:47 , TYR B:48BINDING SITE FOR RESIDUE THU A 138
4AC4SOFTWAREALA A:46 , ALA A:47 , TYR A:48 , PHE B:24 , VAL B:26 , ASN B:42 , GLU B:44 , CYS B:53 , ALA B:54 , GLU B:55 , PRO B:85 , CYS B:86 , CYS B:89 , ZN B:1131BINDING SITE FOR RESIDUE THU B 138

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UX0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UX0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UX0)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.CDD_BACSU1-128
 		  2A:1-128
B:1-128
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.CDD_BACSU53-93
 		  2A:53-93
B:53-93
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.CDD_BACSU1-128
 		  4A:1-128
B:1-128
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.CDD_BACSU53-93
 		  4A:53-93
B:53-93

(-) Exons   (0, 0)

(no "Exon" information available for 1UX0)

(-) 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:130
 aligned with CDD_BACSU | P19079 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
            CDD_BACSU     1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAERTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
               SCOP domains d1ux0a_ A: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1ux0A00 A:1-130 Cytidine Deaminase, domain 2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: A:1-128 UniProt: 1-128                                                                              -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:53-93      ------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux0 A   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with CDD_BACSU | P19079 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
            CDD_BACSU     1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAERTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
               SCOP domains d1ux0b_ B: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1ux0B00 B:1-130 Cytidine Deaminase, domain 2                                                                                       CATH domains
           Pfam domains (1) dCMP_cyt_deam_1-1ux0B01 B:1-105                                                                          ------------------------- Pfam domains (1)
           Pfam domains (2) dCMP_cyt_deam_1-1ux0B02 B:1-105                                                                          ------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: B:1-128 UniProt: 1-128                                                                              -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:53-93      ------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux0 B   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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  (1, 2)

Asymmetric Unit
(-)
Clan: CDA (39)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CDD_BACSU | P19079)
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CDD_BACSU | P19079: 1jtk 1uwz 1ux1

(-) Related Entries Specified in the PDB File

1jtk CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BACILLUS SUBTILIS IN COMPLEX WITH THE INHIBITOR TETRAHYDRODEOXYURIDINE
1uwz CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BACILLUS SUBTILIS R56A MUTANT ENZYME
1ux1 CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BACILLUS SUBTILIS C53H AND R56A MUTANT ENZYME