1I6M - JenaLib

Title :   1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP

Authors :   P. Retailleau, C. W. Carter

Date :   02 Mar 01 (Deposition) - 07 Nov 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

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

Keywords :   Class I Trna Synthetase, Aars, Induced Fit, Trprs, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Retailleau, Y. Yin, M. Hu, J. Roach, G. Bricogne, C. Vonrhein, P. Roversi, E. Blanc, R. M. Sweet, C. W. Carter
High-Resolution Experimental Phases For Tryptophanyl-Trna Synthetase (Trprs) Complexed With Tryptophanyl-5'Amp.
Acta Crystallogr. , Sect. D V. 57 1595 2001
PubMed-ID: 11679724 | Reference-DOI: 10.1107/S090744490101215X

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:160 , LYS A:163 , HOH A:443 , HOH A:550 , HOH A:592	BINDING SITE FOR RESIDUE SO4 A 360
02	AC2	SOFTWARE	THR A:222 , TYR A:265 , LYS A:269 , HOH A:690	BINDING SITE FOR RESIDUE SO4 A 361
03	AC3	SOFTWARE	ARG A:316 , HOH A:673	BINDING SITE FOR RESIDUE SO4 A 362
04	AC4	SOFTWARE	GLY A:264 , TYR A:265 , GLY A:266 , HOH A:529	BINDING SITE FOR RESIDUE SO4 A 363
05	AC5	SOFTWARE	ARG A:182 , MET A:184 , THR A:190 , LYS A:232 , HOH A:498 , HOH A:518	BINDING SITE FOR RESIDUE SO4 A 364
06	AC6	SOFTWARE	LYS A:178 , GLY A:180 , ALA A:181 , ARG A:182 , TYR A:230 , ASN A:243 , HOH A:506	BINDING SITE FOR RESIDUE SO4 A 365
07	AC7	SOFTWARE	ARG A:60 , TYR A:287 , MET A:291 , HOH A:539	BINDING SITE FOR RESIDUE SO4 A 366
08	AC8	SOFTWARE	GLN A:30 , TYR A:33 , GLN A:74 , GOL A:370 , HOH A:570	BINDING SITE FOR RESIDUE NH4 A 400
09	AC9	SOFTWARE	PHE A:5 , SER A:6 , GLY A:7 , ILE A:8 , GLN A:9 , GLY A:17 , ASN A:18 , GLY A:21 , ALA A:22 , VAL A:40 , HIS A:43 , TYR A:125 , MET A:129 , ASP A:132 , ILE A:133 , VAL A:141 , 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 , LYS A:195 , HOH A:402 , HOH A:408 , HOH A:561 , HOH A:593	BINDING SITE FOR RESIDUE TYM A 350
10	BC1	SOFTWARE	ASN A:34 , CYS A:35 , TYR A:36 , GLN A:74 , THR A:76 , LYS A:215 , LYS A:306 , NH4 A:400 , HOH A:477 , HOH A:570	BINDING SITE FOR RESIDUE GOL A 370
11	BC2	SOFTWARE	GLY A:12 , VAL A:13 , ILE A:14 , ARG A:60 , THR A:205 , LEU A:207 , HOH A:706 , HOH A:714	BINDING SITE FOR RESIDUE GOL A 371
12	BC3	SOFTWARE	LYS A:211 , LYS A:215 , LYS A:306 , ARG A:309	BINDING SITE FOR RESIDUE GOL A 372
13	BC4	SOFTWARE	LYS A:192 , SER A:194 , LYS A:195 , SER A:196 , HOH A:593	BINDING SITE FOR RESIDUE GOL A 373

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:326
 aligned with SYW_GEOSE | P00953 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:326
                                    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 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAAKYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGR 326
               SCOP domains d1i6ma_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1i6mA01 A:1-182,A:294-326 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1i6mA02 A:183-293 Tyrosyl-Transfer RNA Synthetase                                                              1i6mA01 A:1-182,A:294-326         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i6m A   1 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGR 326
                                    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 (0, 0)

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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TYM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1i6m)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1i6m
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SYW_GEOSE \| P00953
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	6.1.1.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description