1MAU - JenaLib

Title :   CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH ATP AND TRYPTOPHANAMIDE IN A PRE-TRANSITION STATE CONFORMATION

Authors :   P. Retailleau, X. Huang, Y. Yin, M. Hu, V. Weinreb, P. Vachette, C. Vonrh G. Bricogne, P. Roversi, V. Ilyin, C. W. Carter Jr.

Date :   02 Aug 02 (Deposition) - 07 Jan 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Amino-Acyl Trna Synthetase, Rossmann Fold, Atp Binding Site, Pre- Transition State, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Retailleau, X. Huang, Y. Yin, M. Hu, V. Weinreb, P. Vachette, C. Vonrhein, G. Bricogne, P. Roversi, V. Ilyin, C. W. Carter
Interconversion Of Atp Binding And Conformational Free Energies By Tryptophanyl-Trna Synthetase: Structures Of Atp Bound To Open And Closed, Pre-Transition-State Conformations.
J. Mol. Biol. V. 325 39 2003
PubMed-ID: 12473451 | Reference-DOI: 10.1016/S0022-2836(02)01156-7

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:30 , TYR A:33 , GLN A:74 , HOH A:540 , GOL A:940	BINDING SITE FOR RESIDUE NA A 499
2	AC2	SOFTWARE	LTN A:390 , ATP A:400 , HOH A:613	BINDING SITE FOR RESIDUE MG A 500
3	AC3	SOFTWARE	GLN A:9 , SER A:11 , GLY A:17 , ASN A:18 , GLY A:21 , ALA A:22 , LYS A:111 , VAL A:143 , GLY A:144 , ASP A:146 , GLN A:147 , GLY A:180 , ALA A:181 , ARG A:182 , ILE A:183 , LYS A:192 , MET A:193 , SER A:194 , LYS A:195 , SER A:196 , LTN A:390 , MG A:500 , HOH A:506 , HOH A:524	BINDING SITE FOR RESIDUE ATP A 400
4	AC4	SOFTWARE	PHE A:5 , SER A:6 , GLY A:7 , GLN A:9 , HIS A:43 , GLN A:107 , TYR A:125 , MET A:129 , ASP A:132 , ILE A:133 , VAL A:141 , GLN A:147 , ATP A:400 , MG A:500 , HOH A:613	BINDING SITE FOR RESIDUE LTN A 390
5	AC5	SOFTWARE	SER A:11 , VAL A:47 , TRP A:48 , GLN A:49 , ASP A:50 , SER A:196 , HOH A:581 , HOH A:609 , HOH A:620	BINDING SITE FOR RESIDUE CIT A 1003
6	AC6	SOFTWARE	LYS A:218 , THR A:222 , TYR A:265 , GLY A:266 , LYS A:269	BINDING SITE FOR RESIDUE GOL A 930
7	AC7	SOFTWARE	ASN A:34 , CYS A:35 , TYR A:36 , THR A:73 , GLN A:74 , ALA A:75 , THR A:76 , LYS A:215 , LYS A:306 , NA A:499 , HOH A:559	BINDING SITE FOR RESIDUE GOL A 940
8	AC8	SOFTWARE	TRP A:48 , LYS A:163 , ARG A:164 , LEU A:248	BINDING SITE FOR RESIDUE GOL A 950

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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:328
 aligned with SYW_GEOSE | P00953 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    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        
            SYW_GEOSE     1 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAAKYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGRRR 328
               SCOP domains d1maua_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1mauA01 A:1-182,A:294-326 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1mauA02 A:183-293 Tyrosyl-Transfer RNA Synthetase                                                              1mauA01 A:1-182,A:294-326        -- CATH domains
               Pfam domains tRNA-synt_1b-1mauA01 A:1-281                                                                                                                                                                                                                                                             ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mau A   1 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGRRR 328
                                    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

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, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (SYW_GEOSE | P00953)

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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