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(-) Description

Title :  TRYPTOPHANYL-TRNA SYNTHETASE FROM CRYPTOSPORIDIUM PARVUM
 
Authors :  T. Arakaki, E. A. Merritt
Date :  15 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 206-593
    Gene: CGD7_1490
    Organism Scientific: CRYPTOSPORIDIUM PARVUM IOWA II
    Organism Taxid: 353152

 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
1TRP2Mod. Amino AcidTRYPTOPHAN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:16 , HOH A:38 , TYR A:278 , GLY A:280 , ARG A:281 , GLY A:282 , GLN A:313 , THR A:315 , GLU A:318 , LYS A:319 , GLN A:401 , PRO A:425 , HIS A:426 , GLN A:430 , PHE A:434BINDING SITE FOR RESIDUE TRP A 1
2AC2SOFTWAREHOH B:40 , TYR B:278 , GLY B:280 , ARG B:281 , GLY B:282 , GLN B:313 , THR B:315 , GLU B:318 , LYS B:319 , GLN B:401 , HIS B:426 , GLN B:430 , PHE B:434BINDING SITE FOR RESIDUE TRP B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HV0)

(-) Exons   (0, 0)

(no "Exon" information available for 3HV0)

(-) 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:353
 aligned with Q5CYP8_CRYPI | Q5CYP8 from UniProtKB/TrEMBL  Length:593

    Alignment length:370
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589
         Q5CYP8_CRYPI   220 NKLIDKFGCKLITKDMIERMERLTGQKAHHFFRRNIFLSHRDFEKILDVYEKGELFYLYTGRGPSSESLHVGHLVPFLFTKYLQDTFKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFDPELTFIFTNLEYIAELYPDILRIEKKISCSQIKSIFGFKDSCNVGKFAFPAVQAAPAFSSSFPHIFGGRTDIHCLVPHAIDQDPYFRMVRDVAPRLGYLKPSSIHSIFLPSLQGSQTKMSASVQNSSIFVNDNEESIRNKIMKYAFSGGQATEEEQRRLGANLDVDVSWQYLRFLMEDDEKLEEIGKKYSSGEMLSGEIKSILVQELVKLTKNHQKNREAINDDVIAKFTNKSREQLLKLF 589
               SCOP domains d3hv0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3hv0A01 A:220-459 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                      3hv0A02 A:473-587 Tyrosyl-Transf   er RNA Synthetase                                                                - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhh....eeeee.....-------------........hhhhhhhhhhhhh...........---......hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........-. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hv0 A 220 NKLIDKFGCKLITKDMIERMERLTGQKAHHFFRRNIFLSHRDFEKILDVYEKGELFYLYTGRGPSSESLHVGHLVPFLFTKYLQDTFKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFDPELTFIFTNLEYIAELYPDILRIEKKISCSQIKSIFGFKDSCNVGKFAFPAVQAAPAFSSSFPHIFGGRTDIHCLVPHAIDQDPYFRMVRDVAPRLGYLKPSSIHSIFLPS-------------NSSIFVNDNEESIRNKIMKYAFSGGQATEEEQ---GANLDVDVSWQYLRFLMEDDEKLEEIGKKYSSGEMLSGEIKSILVQELVKLTKNHQKNREAINDDVIAKFTNKSREQLLK-W   1
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         -   |   479       489       499    |  509       519       529       539       549       559       569       579       | 1
                                                                                                                                                                                                                                                                         459           473                            504 508                                                                            587 1


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with Q5CYP8_CRYPI | Q5CYP8 from UniProtKB/TrEMBL  Length:593

    Alignment length:369
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579         
         Q5CYP8_CRYPI   220 NKLIDKFGCKLITKDMIERMERLTGQKAHHFFRRNIFLSHRDFEKILDVYEKGELFYLYTGRGPSSESLHVGHLVPFLFTKYLQDTFKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFDPELTFIFTNLEYIAELYPDILRIEKKISCSQIKSIFGFKDSCNVGKFAFPAVQAAPAFSSSFPHIFGGRTDIHCLVPHAIDQDPYFRMVRDVAPRLGYLKPSSIHSIFLPSLQGSQTKMSASVQNSSIFVNDNEESIRNKIMKYAFSGGQATEEEQRRLGANLDVDVSWQYLRFLMEDDEKLEEIGKKYSSGEMLSGEIKSILVQELVKLTKNHQKNREAINDDVIAKFTNKSREQLLKL 588
               SCOP domains d3hv0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hv0B01 B:220-459 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                      3hv0B02 B:473-587 Tyrosyl-Transf   er RNA Synthetase                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhh....eeeee.....-------------........hhhhhhhhhhhhh...........---......hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hv0 B 220 NKLIDKFGCKLITKDMIERMERLTGQKAHHFFRRNIFLSHRDFEKILDVYEKGELFYLYTGRGPSSESLHVGHLVPFLFTKYLQDTFKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFDPELTFIFTNLEYIAELYPDILRIEKKISCSQIKSIFGFKDSCNVGKFAFPAVQAAPAFSSSFPHIFGGRTDIHCLVPHAIDQDPYFRMVRDVAPRLGYLKPSSIHSIFLPS-------------NSSIFVNDNEESIRNKIMKYAFSGGQATEEEQ---GANLDVDVSWQYLRFLMEDDEKLEEIGKKYSSGEMLSGEIKSILVQELVKLTKNHQKNREAINDDVIAKFTNKSREQLLKW   2
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         -   |   479       489       499    |  509       519       529       539       549       559       569       579       ||
                                                                                                                                                                                                                                                                         459           473                            504 508                                                                            587|
                                                                                                                                                                                                                                                                                                                                                                                                            2
   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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HV0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5CYP8_CRYPI | Q5CYP8)
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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