1TKG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH AN ANALOG OF SERYLADENYLATE

Authors :   A. C. Dock-Bregeon, B. Rees, A. Torres-Larios, G. Bey, J. Caillet, D. Mo

Date :   08 Jun 04 (Deposition) - 30 Nov 04 (Release) - 30 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. Dock-Bregeon, B. Rees, A. Torres-Larios, G. Bey, J. Caillet, D. Moras
Achieving Error-Free Translation; The Mechanism Of Proofreading Of Threonyl-Trna Synthetase At Atomic Resolution.
Mol. Cell V. 16 375 2004
PubMed-ID: 15525511 | Reference-DOI: 10.1016/J.MOLCEL.2004.10.002

Molecule 1 - THREONYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	DOMAINS N1 AND N2 (RESIDUES 1-224)
	Gene	:	THRS, B1719, C2116, SF1512, S1630
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	THREONINE--TRNA LIGASE, THRRS

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SSA	1	Ligand/Ion	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:73 , ALA A:76 , HIS A:77 , ILE A:94 , GLY A:95 , PRO A:96 , TYR A:104 , ILE A:159 , LYS A:169 , PRO A:170 , GLY A:171 , ASP A:180 , MET A:181 , CYS A:182 , ARG A:183 , HOH A:508 , HOH A:517 , HOH A:611	BINDING SITE FOR RESIDUE SSA A 500

(no "SS Bond" information available for 1TKG)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:184	-	Pro A:185

(no "SAP(SNP)/Variant" information available for 1TKG)

(no "PROSITE Motif" information available for 1TKG)

(no "Exon" information available for 1TKG)

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:224
 aligned with SYT_ECOLI | P0A8M3 from UniProtKB/Swiss-Prot  Length:642

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            SYT_ECOLI     1 MPVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWA 224
               SCOP domains d1tkga1 A:1-62                                                d1tkga2 A:63-224 Threonyl-tRNA synthetase (ThrRS), second 'additional' domain                                                                                      SCOP domains
               CATH domains 1tkgA01 A:1-64  [code=3.10.20.30, no name defined]              1tkgA02 A:65-129,A:188-224                                       1tkgA03 A:130-187  [code=3.30.54.20, no name defined]     1tkgA02 A:65-129,A:188-224            CATH domains
               Pfam domains TGS-1tkgA01 A:1-61                                           -------------------------------------------------------------------------------------------------------------tRNA_SAD-1tkgA02 A:171-219                       ----- Pfam domains
         Sec.struct. author ..eee.....eee.....hhhhhhhhhhhhhhhhh.eeee..eeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...ee....ee..eeeeeee.....hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhh......eeeee..eeee.......hhhhh..eeeeeeeeee.hhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tkg A   1 MPVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWA 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ubiquitin (279)

Family: TGS (10)

Escherichia coli (strain K12) (5)

TGS-1tkgA01

A:1-61

Clan: no clan defined [family: tRNA_SAD] (15)

Family: tRNA_SAD (15)

Escherichia coli (strain K12) (5)

tRNA_SAD-1tkgA02

A:171-219

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYT_ECOLI | P0A8M3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	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:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004829	threonine-tRNA ligase activity	Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
	GO:0000900	translation repressor activity, nucleic acid binding	Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0045947	negative regulation of translational initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:184 - Pro A:185	[ RasMol ]

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	1tkg
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	6.1.1.3
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UniProtKB/Swiss-Prot
	SYT_ECOLI \| P0A8M3	:	1evk 1evl 1fyf 1kog 1qf6 1tje 1tke 1tky 4hwo 4hwp 4hwr 4hws 4p3o 4p3p

1qf6	THREONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(THR)
1tje	THE SAME PROTEIN DOMAINS IN THE APO FORM
1tke
1tky

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (20, 20)

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