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(-) Description

Title :  TRYPTOPHANYL-TRNA SYNTHETASE FROM GIARDIA LAMBLIA
 
Authors :  T. L. Arakaki, E. A. Merritt, Medical Structural Genomics Of Patho Protozoa (Msgpp)
Date :  29 Dec 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Tryptophanyl-Trna Synthetase, Giardiasis, Aminoacyl-Trna Synthetase, Ligase, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. L. Arakaki, M. Carter, A. J. Napuli, C. L. Verlinde, E. Fan, F. Zucker F. S. Buckner, W. C. Van Voorhis, W. G. Hol, E. A. Merritt
The Structure Of Tryptophanyl-Trna Synthetase From Giardia Lamblia Reveals Divergence From Eukaryotic Homologs.
J. Struct. Biol. V. 171 238 2010
PubMed-ID: 20438846  |  Reference-DOI: 10.1016/J.JSB.2010.04.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Atcc: 50803
    Chains: A, B
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GL50803_3032
    Organism Scientific: GIARDIA LAMBLIA ATCC 50803
    Organism Taxid: 184922

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:131 , LYS A:135 , ASP A:415 , THR A:416 , HOH A:516BINDING SITE FOR RESIDUE GOL A 502
2AC2SOFTWAREARG A:55 , ARG A:280 , ARG A:283BINDING SITE FOR RESIDUE SO4 A 503
3AC3SOFTWAREPHE B:21 , GLY B:22 , ARG B:55 , ARG B:280BINDING SITE FOR RESIDUE SO4 B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FOC)

(-) 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:404
 aligned with A8B8N3_GIAIC | A8B8N3 from UniProtKB/TrEMBL  Length:429

    Alignment length:429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420         
         A8B8N3_GIAIC     1 METDATAEAAAVAYEDIITRFGAAPITDDLLKRFETVTGTKAHPMLRRGLFYAHRDFEEFLSYYEKGHPIYIYTGRGPSSGALHLGHLLPFIFTKYLQDAFKCYVVIQITDDEKFLRNRSLSYAEVDSYTRENIKDIIACGFDPDKTFIFINSQYLSLKNRYRFSCLVDRMLPISQLRASFGFSNDANVGYAAFPPKQMLPVYSTYFDGLPFTRVPLPVGTGNEDAADAVSTKKASKKTPKKDAVLSPVHVVEELFPDSKRYQKAMCLIASGIEQDPYFRLARDLAPRMGHPKNAYLLGKFLPGLQGSGTKMSASDPNSAIYLTDTPAQIKNKINRYAFSGGRDTEEEHRAFGADLSVDVSVRYLEVFMKDDAELEKLKADYKAGKLLTGEVKATLIGILQGLIKEHAERRDKVDTTMIESFTVKKELQ 429
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3focA01 A:1-316 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                       3focA02 A:317-424 Tyrosyl-Transfer RNA Synthetase                                                           ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhh...hhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhh....-------------------------...hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh........eeeee................hhhhh.....hhhhhhhhhhhhh......hhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foc A   1 METDATAEAAAVAYEDIITRFGAAPITDDLLKRFETVTGTKAHPMLRRGLFYAHRDFEEFLSYYEKGHPIYIYTGRGPSSGALHLGHLLPFIFTKYLQDAFKCYVVIQITDDEKFLRNRSLSYAEVDSYTRENIKDIIACGFDPDKTFIFINSQYLSLKNRYRFSCLVDRMLPISQLRASFGFSNDANVGYAAFPPKQMLPVYSTYFDGLPFTRVPLP-------------------------AVLSPVHVVEELFPDSKRYQKAMCLIASGIEQDPYFRLARDLAPRMGHPKNAYLLGKFLPGLQGSGTKMSASDPNSAIYLTDTPAQIKNKINRYAFSGGRDTEEEHRAFGADLSVDVSVRYLEVFMKDDAELEKLKADYKTGKLLTGEVKATLIGILQGLIKEHAERRDKVDTTMIESFTVKKELQ 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       | -         -         -   |   250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420         
                                                                                                                                                                                                                                                   218                       244                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:399
 aligned with A8B8N3_GIAIC | A8B8N3 from UniProtKB/TrEMBL  Length:429

    Alignment length:427
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       
         A8B8N3_GIAIC     3 TDATAEAAAVAYEDIITRFGAAPITDDLLKRFETVTGTKAHPMLRRGLFYAHRDFEEFLSYYEKGHPIYIYTGRGPSSGALHLGHLLPFIFTKYLQDAFKCYVVIQITDDEKFLRNRSLSYAEVDSYTRENIKDIIACGFDPDKTFIFINSQYLSLKNRYRFSCLVDRMLPISQLRASFGFSNDANVGYAAFPPKQMLPVYSTYFDGLPFTRVPLPVGTGNEDAADAVSTKKASKKTPKKDAVLSPVHVVEELFPDSKRYQKAMCLIASGIEQDPYFRLARDLAPRMGHPKNAYLLGKFLPGLQGSGTKMSASDPNSAIYLTDTPAQIKNKINRYAFSGGRDTEEEHRAFGADLSVDVSVRYLEVFMKDDAELEKLKADYKAGKLLTGEVKATLIGILQGLIKEHAERRDKVDTTMIESFTVKKELQ 429
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3focB01 B:3-316 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                     3focB02 B:317-424 Tyrosyl-Tra     nsfer RNA Synthetase                                                      ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhh...hhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhh......-----------------------...hhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh........eeeee................hhhhh.....hhhhhhhhhhhhh.......-----........hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foc B   3 TDATAEAAAVAYEDIITRFGAAPITDDLLKRFETVTGTKAHPMLRRGLFYAHRDFEEFLSYYEKGHPIYIYTGRGPSSGALHLGHLLPFIFTKYLQDAFKCYVVIQITDDEKFLRNRSLSYAEVDSYTRENIKDIIACGFDPDKTFIFINSQYLSLKNRYRFSCLVDRMLPISQLRASFGFSNDANVGYAAFPPKQMLPVYSTYFDGLPFTRVPLPVG-----------------------AVLSPVHVVEELFPDSKRYQKAMCLIASGIEQDPYFRLARDLAPRMGHPKNAYLLGKFLPGLQGSGTKMSASDPNSAIYLTDTPAQIKNKINRYAFSGGRDT-----AFGADLSVDVSVRYLEVFMKDDAELEKLKADYKTGKLLTGEVKATLIGILQGLIKEHAERRDKVDTTMIESFTVKKELQ 429
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       | -         -         - |     252       262       272       282       292       302       312       322       332       342  |    352       362       372       382       392       402       412       422       
                                                                                                                                                                                                                                                   220                     244                                                                                                  345   351
   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 3FOC)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A8B8N3_GIAIC | A8B8N3)
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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