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(-) Description

Title :  TRYPTOPHANYL-TRNA SYNTHETASE VAL144PRO MUTANT FROM B. SUBTILIS
 
Authors :  A. K. Antonczak, Z. Simova, I. Yonemoto, M. Bochtler, A. Piasecka, H. Cz A. Brancale, E. M. Tippmann
Date :  29 Nov 10  (Deposition) - 19 Jan 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trprs, Protein Biosynthesis, Translation, Class I Trna Synthetase, Rossmann Fold, High Motif, Kmsks Motif, Aminoacyl-Trna Synthetase, Ligase, Atp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Antonczak, Z. Simova, I. T. Yonemoto, M. Bochtler, A. Piasecka, H. Czapinska, A. Brancale, E. M. Tippmann
Importance Of Single Molecular Determinants In The Fidelity Of Expanded Genetic Codes.
Proc. Natl. Acad. Sci. Usa V. 108 1320 2011
PubMed-ID: 21224416  |  Reference-DOI: 10.1073/PNAS.1012276108

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    ChainsA, B
    EC Number6.1.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET151/D-TOPO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Gene939361, BSU11420, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI, TRPS
    MutationYES
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    Strain168
    SynonymTRYPTOPHAN-TRNA LIGASE, TRPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3PRH)

(-) Sites  (0, 0)

(no "Site" information available for 3PRH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_BACSU11-20
 
  2A:11-20
B:11-20

(-) Exons   (0, 0)

(no "Exon" information available for 3PRH)

(-) 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:316
 aligned with SYW_BACSU | P21656 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
            SYW_BACSU     2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMTQFKDKSKGNEAVVSGLLTYPPLMAADILLYGTDLVPVGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
               SCOP domains d3prha_ A: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhh..----------..hhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhh.......ee..................................hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prh A   2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMT----------AVVSGLLTYPPLMAADILLYGTDLVPPGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
                                    11        21        31        41        51        61        71        81        91       101     |   -      |121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                   107        118                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with SYW_BACSU | P21656 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
            SYW_BACSU     2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMTQFKDKSKGNEAVVSGLLTYPPLMAADILLYGTDLVPVGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
               SCOP domains d3prhb_ B: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) tRNA-synt_1b-3prhB01 B:2-282                                                                                                                                                                                                                                                             --------------------------------------------- Pfam domains (1)
           Pfam domains (2) tRNA-synt_1b-3prhB02 B:2-282                                                                                                                                                                                                                                                             --------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh..hhhhhhh.-------------hhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhh.......ee..----............................hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prh B   2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERM-------------VSGLLTYPPLMAADILLYGTDLVPPGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKI----ARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
                                    11        21        31        41        51        61        71        81        91       101    |    -       121       131       141       151       161       171     |   -|      191       201       211       221       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                  106           120                                                      177  182                                                                                                                                                 

   Legend:   → Mismatch (orange background)
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    → 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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYW_BACSU | P21656)
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: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:0004830    tryptophan-tRNA ligase activity    Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
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: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.
    GO:0006436    tryptophanyl-tRNA aminoacylation    The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-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.
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)

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(-) Related Entries Specified in the PDB File

1d2r 2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE
1m83 CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH ATP IN A CLOSED, PRE-TRANSITION STATE CONFORMATION
1mau CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH ATP AND TRYPTOPHANAMIDE IN A PRE-TRANSITION STATE CONFORMATION
1maw CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN IN AN OPEN CONFORMATION
1mb2 CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN IN AN OPEN CONFORMATION
2ov4 CRYSTAL STRUCTURE OF B. STEAROTHERMOPHILUS TRYPTOPHANYL TRNA SYNTHETASE IN COMPLEX WITH ADENOSINE TETRAPHOSPHATE
3fi0 CRYSTAL STRUCTURE ANALYSIS OF B. STEAROTHERMOPHILUS TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN, AMP, AND INORGANIC PHOSPHATE