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Title :   CRYSTAL STRUCTURE OF THE APO FORM OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE DETERMINED AT 2.1 ANGSTROM RESOLUTION

Authors :   K. M. Peterson, J. Ling, I. Simonovic, C. Cho, D. Soll, M. Simonovic

Date :   02 Nov 11 (Deposition) - 22 Feb 12 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Trna, Threonyl-Trna Synthetase, Threonine Trna, Aminoacyl-Trna Synthetase Class Ii, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ling, K. M. Peterson, I. Simonovic, C. Cho, D. Soll, M. Simonovic
Yeast Mitochondrial Threonyl-Trna Synthetase Recognizes Trn Isoacceptors By Distinct Mechanisms And Promotes Cun Codon Reassignment.
Proc. Natl. Acad. Sci. Usa V. 109 3281 2012
PubMed-ID: 22343532 | Reference-DOI: 10.1073/PNAS.1200109109

Molecule 1 - THREONYL-TRNA SYNTHETASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	6.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-462
	Gene	:	MST1, YKL194C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	THREONINE--TRNA LIGASE, THRRS

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION
2	SO4	6	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	SO4	12	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:133 , HIS A:184 , HIS A:319 , K A:469	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	ARG A:153 , HOH A:521	BINDING SITE FOR RESIDUE SO4 A 463
3	AC3	SOFTWARE	ARG A:162 , LYS A:273 , GLN A:287 , GLN A:292 , HOH A:665 , HOH A:701	BINDING SITE FOR RESIDUE SO4 A 2
4	AC4	SOFTWARE	ARG A:231 , GLU A:424 , HOH A:752	BINDING SITE FOR RESIDUE SO4 A 464
5	AC5	SOFTWARE	GLY A:237 , ARG A:300 , SO4 A:467	BINDING SITE FOR RESIDUE SO4 A 465
6	AC6	SOFTWARE	PHE A:225 , ASN A:227 , LYS A:261 , THR A:285	BINDING SITE FOR RESIDUE SO4 A 466
7	AC7	SOFTWARE	GLU A:101 , GLY A:104 , ASN A:108 , ARG A:300 , SO4 A:465 , HOH A:519	BINDING SITE FOR RESIDUE SO4 A 467
8	AC8	SOFTWARE	ZN A:1	BINDING SITE FOR RESIDUE K A 469

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

Asymmetric Unit

No.	Residues
1	Leu A:150	-	Pro A:151

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

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

(no "Exon" information available for 3UGQ)

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:426
 aligned with SYTM_YEAST | P07236 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:430
                                    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       432       442       452       462
           SYTM_YEAST    33 ATPATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTDEEKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPFVKGGSGAESNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh....eeee.......eeee...hhhhhhhhhhhh..hhhhh.eeeeeeeeee...hhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....----.....eeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeee...hhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.......eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ugq A  33 ATPATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTDEEKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPFV----GAESNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    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       432       442       452       462
                                                                                                                                                                                                               214  219

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 '\|'

(no "SCOP Domain" information available for 3UGQ)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (SYTM_YEAST | P07236)

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: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:0004829	threonine-tRNA ligase activity	Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
biological process
	GO:0070159	mitochondrial threonyl-tRNA aminoacylation	The process of coupling threonine to threonyl-tRNA in a mitochondrion, 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: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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:150 - Pro A:151	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3ugq
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	6.1.1.3
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	SYTM_YEAST \| P07236	:	3ugt 3uh0 4eo4 4yye

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (13, 13)

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