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(-) Description

Title :  TRYPTOPHANYL-TRNA SYNTHETASE FROM TRYPANOSOMA BRUCEI
 
Authors :  T. Arakaki, E. A. Merritt
Date :  24 Jun 09  (Deposition) - 28 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apo Trna-Ligase, Atp-Binding, Aminoacyl-Trna Synthetase, Ligase, Nucleotide-Binding, Protein Biosynthesis, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Merritt, T. L. Arakaki, R. Gillespie, A. J. Napuli, J. E. Kim, F. S. Buckner, W. C. Van Voorhis, C. L. Verlinde, E. Fan, F. Zucker, W. G. Hol
Crystal Structures Of Three Protozoan Homologs Of Tryptophanyl-Trna Synthetase.
Mol. Biochem. Parasitol. V. 177 20 2011
PubMed-ID: 21255615  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2011.01.003

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BG1861
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-389
    Gene: TB927.3.5580
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 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 3I05)

(-) Sites  (0, 0)

(no "Site" information available for 3I05)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I05)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I05)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I05)

(-) Exons   (0, 0)

(no "Exon" information available for 3I05)

(-) 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:328
 aligned with Q580R7_TRYB2 | Q580R7 from UniProtKB/TrEMBL  Length:389

    Alignment length:370
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385
         Q580R7_TRYB2    16 NYDKLIKDFGSHAIDEALLERIERVLGKKPHHFLRRGIFFSHRDLNLLLDVYESGQPFYLYTGRGPSSESMHMGHLIPFMFTKWLQDSFRVPLVIQMTDDEKFYFRNIPMEQVEAMTTENIKDIIAMGFDPELTFIFRDFDYMGCMYRTVAKIERAFTASQVRGCFGFAMEDNCGRWMFPAIQAAPSFSAAFPHIFPPSMGNVFCLIPQAIDQDPYFRLTRDIAPRLGYLKPAVIHSKFFPGLSGPKGKMSSSSGTAVLLTDTEKMVKDKINKHAFSGGGATKQEHFLLGANVEVDVPIQWLSFFLEDDEELARVKKEYMLGRIMTGEVKKLLINTITAITKTHQEKRKLVTDEDVQLFTSTRIMGPAKK 385
               SCOP domains d3i05a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhh..eeeeeee..hhhhhhhhhhhhhhhh....eeeee......-------------......hhhhhhhhhh----------------------.hhhhhhhhhhh..hhhhhhhh.-------hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i05 A  16 NYDKLIKDFGSHAIDEALLERIERVLGKKPHHFLRRGIFFSHRDLNLLLDVYESGQPFYLYTGRGPSSESMHMGHLIPFMFTKWLQDSFRVPLVIQMTDDEKFYFRNIPMEQVEAMTTENIKDIIAMGFDPELTFIFRDFDYMGCMYRTVAKIERAFTASQVRGCFGFAMEDNCGRWMFPAIQAAPSFSAAFPHIFPPSMGNVFCLIPQAIDQDPYFRLTRDIAPRLGYLKPAVIHSKFFPGL-------------AVLLTDTEKMVKDKIN----------------------VDVPIQWLSFFLEDDEELARVKK-------MTGEVKKLLINTITAITKTHQEKRKLVTDEDVQLFTSTRIMGPAKK 385
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  |      -      |275       285 |       -         -    |  315       325      |  -    |  345       355       365       375       385
                                                                                                                                                                                                                                                                            258           272            287                    310                   332     340                                             


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with Q580R7_TRYB2 | Q580R7 from UniProtKB/TrEMBL  Length:389

    Alignment length:370
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385
         Q580R7_TRYB2    16 NYDKLIKDFGSHAIDEALLERIERVLGKKPHHFLRRGIFFSHRDLNLLLDVYESGQPFYLYTGRGPSSESMHMGHLIPFMFTKWLQDSFRVPLVIQMTDDEKFYFRNIPMEQVEAMTTENIKDIIAMGFDPELTFIFRDFDYMGCMYRTVAKIERAFTASQVRGCFGFAMEDNCGRWMFPAIQAAPSFSAAFPHIFPPSMGNVFCLIPQAIDQDPYFRLTRDIAPRLGYLKPAVIHSKFFPGLSGPKGKMSSSSGTAVLLTDTEKMVKDKINKHAFSGGGATKQEHFLLGANVEVDVPIQWLSFFLEDDEELARVKKEYMLGRIMTGEVKKLLINTITAITKTHQEKRKLVTDEDVQLFTSTRIMGPAKK 385
               SCOP domains d3i05b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhh..eeeeeee..hhhhhhhhhhhhhhhh....eeeee.......------------......hhhhhhhhhh.------------------------hhhhhhhhh.hhhhhhhhh..---...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i05 B  16 NYDKLIKDFGSHAIDEALLERIERVLGKKPHHFLRRGIFFSHRDLNLLLDVYESGQPFYLYTGRGPSSESMHMGHLIPFMFTKWLQDSFRVPLVIQMTDDEKFYFRNIPMEQVEAMTTENIKDIIAMGFDPELTFIFRDFDYMGCMYRTVAKIERAFTASQVRGCFGFAMEDNCGRWMFPAIQAAPSFSAAFPHIFPPSMGNVFCLIPQAIDQDPYFRLTRDIAPRLGYLKPAVIHSKFFPGLS------------AVLLTDTEKMVKDKINK------------------------PIQWLSFFLEDDEELARVKKE---GRIMTGEVKKLLINTITAITKTHQEKRKLVTDEDVQLFTSTRIMGPAKK 385
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   |     -      |275       285  |      -         -       315       325       | - |     345       355       365       375       385
                                                                                                                                                                                                                                                                             259          272             288                      313                 333 337
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I05)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q580R7_TRYB2 | Q580R7)
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3hv0 3hzr