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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE TRNA-SPECIFIC ADENOSINE DEAMINASE FROM STREPTOCOCCUS PYOGENES
 
Authors :  K. Y. Hwang, W. -H. Lee, Y. K. Kim
Date :  17 Nov 06  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Trna, Adenosine, Deaminase, Tad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. -H. Lee, Y. K. Kim, K. H. Nam, A. Priyadarshi, E. H. Lee, E. E. Kim, Y. H. Jeon, C. Cheong, K. Y. Hwang
Crystal Structure Of The Trna-Specific Adenosine Deaminase From Streptococcus Pyogenes
Proteins V. 68 1016 2007
PubMed-ID: 17554781  |  Reference-DOI: 10.1002/PROT.21456

(-) Compounds

Molecule 1 - TRNA-SPECIFIC ADENOSINE DEAMINASE
    Chains: A
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 22B
    Expression System Strain: BL 21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M6
    Organism Taxid: 301450
    Strain: MGAS10394
    Synonym: HYPOTHETICAL PROTEIN M6_SPY0214

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2NX8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NX8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NX8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NX8)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.TADA_STRP66-133  1A:14-141
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.TADA_STRP657-94  1A:65-102
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.TADA_STRP66-133  2A:14-141
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.TADA_STRP657-94  2A:65-102

(-) Exons   (0, 0)

(no "Exon" information available for 2NX8)

(-) 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:168
 aligned with TADA_STRP6 | Q5XE14 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:168
                               1                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157        
           TADA_STRP6     - ---MPYSLEEQTYFMQEALKEAEKSLQKAEIPIGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFVTIEPCVMCSGAIGLARIPHVIYGASNQKFGGADSLYQILTDERLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHLIKE 165
               SCOP domains d2nx8a_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------dCMP_cyt_deam_1-2nx8A01 A:13-114                                                                      ----------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhh...eeeeee............hhhhh.......eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------CYT_DCMP_DEAMINASES_2  PDB: A:14-141 UniProt: 6-133                                                                             -------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:65-102  ----------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nx8 A   6 SFLMPYSLEEQTYFMQEALKESEKSLQKAEIPIGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFVTIEPCVMCSGAIGLARIPHVIYGASNQKFGGVDSLYQILTDERLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHLIKE 173
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NX8)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: CDA (39)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TADA_STRP6 | Q5XE14)
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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