3KT0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF S. CEREVISIAE TRYPTOPHANYL-TRNA SYNTHETASE

Authors :   M. Zhou, X. Dong, C. Zhong, N. Shen, J. Ding

Date :   24 Nov 09 (Deposition) - 16 Feb 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Tryptophanyl-Trna Synthetase, Rossmann Fold, S. Cerevisiae, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zhou, X. Dong, N. Shen, C. Zhong, J. Ding
Crystal Structures Of Saccharomyces Cerevisiae Tryptophanyl-Trna Synthetase: New Insights Into The Mechanism Of Tryptophan Activation And Implications For Anti-Fungal Drug Design
Nucleic Acids Res. V. 38 3399 2010
PubMed-ID: 20123733 | Reference-DOI: 10.1093/NAR/GKP1254

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE, CYTOPLASMIC
	Chains	:	A
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3E
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPS
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	TRYPTOPHAN--TRNA LIGASE, TRPRS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	EMN	1	Ligand/Ion	(2S)-1-{[(2S)-3-(2-METHOXYETHOXY)-2-METHYLPROPYL]OXY}PROPAN-2-AMINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	EMN	2	Ligand/Ion	(2S)-1-{[(2S)-3-(2-METHOXYETHOXY)-2-METHYLPROPYL]OXY}PROPAN-2-AMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:106 , THR A:107 , GLY A:108 , THR A:143 , GLN A:259	BINDING SITE FOR RESIDUE EMN A 439

(no "SS Bond" information available for 3KT0)

(no "Cis Peptide Bond" information available for 3KT0)

(no "SAP(SNP)/Variant" information available for 3KT0)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_YEAST	111-121	1	A:111-121

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_YEAST	111-121	2	A:111-121

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOL097C	1	YOL097C.1	XV:137825-136527	1299	SYWC_YEAST	1-432	432	1	A:45-425 (gaps)	381

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
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Chain A from PDB  Type:PROTEIN  Length:373
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:381
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424 
           SYWC_YEAST    45 IDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
               SCOP domains d3kt0a_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt0A01 A:246-389                                                                                                                  ------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt0A02 A:246-389                                                                                                                  ------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhhhhh....eeeee........--------..........hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------AA_TRNA_LIG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:45-425 (gaps) UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 3kt0 A  45 IDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQG--------DDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      |  -     | 304       314       324       334       344       354       364       374       384       394       404       414       424 
                                                                                                                                                                                                                                                                                291      300

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 "CATH Domain" information available for 3KT0)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	tRNA-synt_1b-3kt0A01	A:246-389
1b	tRNA-synt_1b-3kt0A02	A:246-389

Asymmetric Unit(hide GO term definitions)

Chain A (SYWC_YEAST | Q12109)

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.

Asymmetric Unit
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Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3kt0
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	6.1.1.2
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UniProtKB/Swiss-Prot
	SYWC_YEAST \| Q12109	:	2ip1 3kt3 3kt6 3kt8

3kt3	THE SAME PROTEIN IN COMPLEX WITH TRPAMP
3kt6	THE SAME PROTEIN IN COMPLEX WITH TRP
3kt8	THE SAME PROTEIN IN COMPLEX WITH L-TRYPTOPHANAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

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Gene Ontology (9, 9)

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