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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  27 Apr 10  (Deposition) - 19 May 10  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Mycobacterium Smegmatis, Cytidine Deaminase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE
    ChainsA, B, C, D
    EC Number3.5.4.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidAVA0421
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCDD, MSMEG_1673
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid246196
    StrainATCC 700084 / MC(2)155

 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:53 , CYS A:86 , CYS A:89 , HOH A:327BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWARECYS B:53 , CYS B:86 , CYS B:89 , HOH B:347BINDING SITE FOR RESIDUE ZN B 300
3AC3SOFTWARECYS C:53 , CYS C:86 , CYS C:89 , HOH C:364BINDING SITE FOR RESIDUE ZN C 300
4AC4SOFTWARECYS D:53 , CYS D:86 , CYS D:89 , HOH D:377BINDING SITE FOR RESIDUE ZN D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MPZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:-2 -Ser A:-1

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MPZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MPZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3MPZ)

(-) 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:125
 aligned with A0QT11_MYCS2 | A0QT11 from UniProtKB/TrEMBL  Length:128

    Alignment length:125
                               1                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117     
         A0QT11_MYCS2     - ---MNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFGP 122
               SCOP domains d3mpza_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......eehhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpz A  -2 GSMVNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFGP 122
                                     7        17        27        37        47        57        67        77        87        97       107       117     

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with A0QT11_MYCS2 | A0QT11 from UniProtKB/TrEMBL  Length:128

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
         A0QT11_MYCS2     1 MNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFG 121
               SCOP domains d3mpzb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......ee.hhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpz B   1 VNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with A0QT11_MYCS2 | A0QT11 from UniProtKB/TrEMBL  Length:128

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
         A0QT11_MYCS2     1 MNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFGPD 123
               SCOP domains d3mpzc_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......eehhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpz C   1 VNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAFGPD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with A0QT11_MYCS2 | A0QT11 from UniProtKB/TrEMBL  Length:128

    Alignment length:122
                              1                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118  
         A0QT11_MYCS2     - --MNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAF 120
               SCOP domains d3mpzd_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---dCMP_cyt_deam_1-3mpzD01 D:2-105                                                                         --------------- Pfam domains (1)
           Pfam domains (2) ---dCMP_cyt_deam_1-3mpzD02 D:2-105                                                                         --------------- Pfam domains (2)
           Pfam domains (3) ---dCMP_cyt_deam_1-3mpzD03 D:2-105                                                                         --------------- Pfam domains (3)
           Pfam domains (4) ---dCMP_cyt_deam_1-3mpzD04 D:2-105                                                                         --------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......eehhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpz D  -1 SMVNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVGPDGGVLMPCGRCRQVLLEHGGPELLIDHAHGPRPLRELLPDAF 120
                                     8        18        28        38        48        58        68        78        88        98       108       118  

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MPZ)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (A0QT11_MYCS2 | A0QT11)
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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