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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM PYROCOCCUS ABYSSI IN COMPLEX WITH SERYL-3'-AMINOADENOSINE
 
Authors :  T. Hussain, V. Kamarthapu, S. P. Kruparani, R. Sankaranarayanan
Date :  22 Oct 10  (Deposition) - 08 Dec 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Fold, Deacylase, Editing, Aminoacyl-Trna Synthetase, Translation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hussain, V. Kamarthapu, S. P. Kruparani, M. V. Deshmukh, R. Sankaranarayanan
Mechanistic Insights Into Cognate Substrate Discrimination During Proofreading In Translation
Proc. Natl. Acad. Sci. Usa V. 107 22117 2010
PubMed-ID: 21098258  |  Reference-DOI: 10.1073/PNAS.1014299107

(-) Compounds

Molecule 1 - THREONYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-147
    Gene: PAB1490, PYRAB13430, THRS
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: THREONINE--TRNA LIGASE, THRRS

 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
1A3S2Ligand/IonSERINE-3'-AMINOADENOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:19 , ILE A:43 , VAL A:45 , PRO A:80 , PHE A:81 , ALA A:82 , ALA A:89 , ALA A:94 , PHE A:117 , GLY A:118 , TYR A:119 , TYR A:120 , LYS A:121 , HOH A:1011 , HOH A:1020 , HOH A:1022 , GLU B:134 , HOH B:1002 , HOH B:1005BINDING SITE FOR RESIDUE A3S A 500
2AC2SOFTWAREGLU A:134 , HOH A:1001 , HOH A:1025 , ALA B:19 , LEU B:20 , ILE B:43 , SER B:44 , VAL B:45 , PRO B:80 , PHE B:81 , ALA B:82 , LEU B:88 , ALA B:89 , ALA B:94 , PHE B:117 , GLY B:118 , TYR B:119 , TYR B:120 , LYS B:121 , HOH B:1042 , HOH B:1161BINDING SITE FOR RESIDUE A3S B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PD2)

(-) Exons   (0, 0)

(no "Exon" information available for 3PD2)

(-) 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:147
 aligned with SYT_PYRAB | Q9UZ14 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
            SYT_PYRAB     1 MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEEARVE 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee........hhhh.eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pd2 A   1 MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEEARVE 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with SYT_PYRAB | Q9UZ14 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
            SYT_PYRAB     1 MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE 143
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) tRNA-Thr_ED-3pd2B01 B:1-139                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) tRNA-Thr_ED-3pd2B02 B:1-139                                                                                                                ---- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeeeeee........hhhh.eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pd2 B   1 MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (0, 0)

(no "SCOP Domain" information available for 3PD2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PD2)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: tRNA-Thr_ED] (5)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYT_PYRAB | Q9UZ14)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004829    threonine-tRNA ligase activity    Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006435    threonyl-tRNA aminoacylation    The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT_PYRAB | Q9UZ14: 1y2q 2hkz 2hl0 2hl1 2hl2 3pd3 3pd4 3pd5 4rrq 4rrr 4s02 4s03 4s0i 4s0j 4s0k 4s0l

(-) Related Entries Specified in the PDB File

1y2q 2hl0 2hl1 2hl2 3pd3 3pd4 3pd5