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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA ADENOSINE DEAMINASE TADA FROM ESCHERICHIA COLI
 
Authors :  V. Malashkevich, J. Kim, M. Lisbin, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Mar 05  (Deposition) - 21 Feb 06  (Release) - 30 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trna Adenosine Deaminase, Dimer, Zinc, Metalloenzyme, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kim, V. Malashkevich, S. Roday, M. Lisbin, V. L. Schramm, S. C. Almo
Structural And Kinetic Characterization Of Escherichia Coli Tada, The Wobble-Specific Trna Deaminase.
Biochemistry V. 45 6407 2006
PubMed-ID: 16700551  |  Reference-DOI: 10.1021/BI0522394
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA-SPECIFIC ADENOSINE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: TADA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , CYS A:98 , CYS A:101 , HOH A:416BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS B:68 , CYS B:98 , CYS B:101 , HOH B:413BINDING SITE FOR RESIDUE ZN B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z3A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z3A)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.TADA_ECOLI6-117
 		  2A:17-128
B:17-128
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.TADA_ECOLI57-94
 		  2A:68-105
B:68-105

(-) Exons   (0, 0)

(no "Exon" information available for 1Z3A)

(-) 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:156
 aligned with TADA_ECOLI | P68398 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           TADA_ECOLI     2 SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK 157
               SCOP domains d1z3aa1 A:13-168 tRNA adenosine deaminase TadA                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeee........................eee...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----CYT_DCMP_DEAMINASES_2  PDB: A:17-128 UniProt: 6-117                                                             ---------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:68-105  --------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z3a A  13 SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK 168
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with TADA_ECOLI | P68398 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           TADA_ECOLI     2 SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK 157
               SCOP domains d1z3ab_ B: tRNA adenosine deaminase TadA                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---dCMP_cyt_deam_1-1z3aB01 B:16-117                                                                      --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---dCMP_cyt_deam_1-1z3aB02 B:16-117                                                                      --------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeee........................eeee..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----CYT_DCMP_DEAMINASES_2  PDB: B:17-128 UniProt: 6-117                                                             ---------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:68-105  --------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z3a B  13 SEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIK 168
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z3A)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TADA_ECOLI | P68398)
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: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:0008251    tRNA-specific adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a tRNA molecule.
    GO:0052717    tRNA-specific adenosine-34 deaminase activity    Catalysis of the reaction: adenosine-34 + H2O = inosine-34 + NH3, in a tRNA-Ala molecule.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002100    tRNA wobble adenosine to inosine editing    The process in which an adenosine in position 34 of a tRNA is post-transcriptionally converted to inosine.

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