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(-) Description

Title :  BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH A CYS53HIS AND AN ARG56GLN 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 :  2.36
Chains :  Asym./Biol. Unit :  A,B,C,D
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, C, D
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCC53H/R56QCDA
    Expression System Strain: SO5201
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: CYTIDINE AMINOHYDROLASE, CDA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1THU4Ligand/IonTETRAHYDRODEOXYURIDINE
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:53 , CYS A:86 , CYS A:89 , THU A:138BINDING SITE FOR RESIDUE ZN A1132
2AC2SOFTWAREHIS B:53 , CYS B:86 , CYS B:89 , THU B:138BINDING SITE FOR RESIDUE ZN B1131
3AC3SOFTWAREHIS C:53 , CYS C:86 , CYS C:89 , THU C:138BINDING SITE FOR RESIDUE ZN C1131
4AC4SOFTWAREHIS D:53 , CYS D:86 , CYS D:89 , THU D:138BINDING SITE FOR RESIDUE ZN D1132
5AC5SOFTWARESER A:22 , PHE A:24 , VAL A:26 , ASN A:42 , GLU A:44 , HIS A:53 , ALA A:54 , GLU A:55 , PRO A:85 , CYS A:86 , CYS A:89 , ZN A:1132 , ALA C:46BINDING SITE FOR RESIDUE THU A 138
6AC6SOFTWAREASP A:15 , ALA A:17 , GLN A:25 , ASP C:15 , GLN C:25BINDING SITE FOR RESIDUE TRS A1133
7AC7SOFTWARESER B:22 , PHE B:24 , VAL B:26 , ASN B:42 , GLU B:44 , HIS B:53 , ALA B:54 , GLU B:55 , PRO B:85 , CYS B:86 , CYS B:89 , ZN B:1131 , ALA D:46BINDING SITE FOR RESIDUE THU B 138
8AC8SOFTWAREALA A:46 , ALA A:47 , TYR A:48 , PHE C:24 , VAL C:26 , ASN C:42 , GLU C:44 , HIS C:53 , ALA C:54 , GLU C:55 , PRO C:85 , CYS C:86 , CYS C:89 , ZN C:1131 , PHE D:125BINDING SITE FOR RESIDUE THU C 138
9AC9SOFTWAREALA B:46 , ALA B:47 , TYR B:48 , PHE D:24 , VAL D:26 , ASN D:42 , GLU D:44 , HIS D:53 , ALA D:54 , GLU D:55 , PRO D:85 , CYS D:86 , CYS D:89 , ZN D:1132BINDING SITE FOR RESIDUE THU D 138

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UX1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UX1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UX1)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.CDD_BACSU1-128
 
 
 		  4A:1-128
B:1-128
C:1-128
D:1-128
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.CDD_BACSU53-93
 
 
 		  4A:54-93
B:54-93
C:54-93
D:54-93

(-) Exons   (0, 0)

(no "Exon" information available for 1UX1)

(-) 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:131
 aligned with CDD_BACSU | P19079 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
            CDD_BACSU     1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAERTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDLH 131
               SCOP domains d1ux1a_ A: mono-domain cytidine deaminase                                                                                           SCOP domains
               CATH domains 1ux1A00 A:1-131 Cytidine Deaminase, domain 2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhhh 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:54-93      -------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux1 A   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNHAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDLH 131
                                    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 d1ux1b_ B: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1ux1B00 B:1-130 Cytidine Deaminase, domain 2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhh.....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:54-93      ------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux1 B   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNHAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain C 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 d1ux1c_ C: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1ux1C00 C:1-130 Cytidine Deaminase, domain 2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: C:1-128 UniProt: 1-128                                                                              -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:54-93      ------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux1 C   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNHAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDL 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with CDD_BACSU | P19079 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
            CDD_BACSU     1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAERTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDLH 131
               SCOP domains d1ux1d_ D: mono-domain cytidine deaminase                                                                                           SCOP domains
               CATH domains 1ux1D00 D:1-131 Cytidine Deaminase, domain 2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhh....eeeeee....eeeeehhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: D:1-128 UniProt: 1-128                                                                              --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:54-93      -------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux1 D   1 MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNHAEQTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDLH 131
                                    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)
    → 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  (0, 0)

(no "Pfam Domain" information available for 1UX1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1ux1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDD_BACSU | P19079: 1jtk 1uwz 1ux0

(-) Related Entries Specified in the PDB File

1jtk CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BACILLUSSUBTILIS IN COMPLEX WITH THE INHIBITOR TETRAHYDRODEOXYURIDINE
1uwz BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56 TO ALA SUBSTITUTION
1ux0 BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56 TO GLN SUBSTITUTION