1QU2 | PR0014 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN

Authors :   L. F. Silvian, J. Wang, T. A. Steitz

Date :   06 Jul 99 (Deposition) - 31 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,T

Keywords :   Protein-Rna Complex, Metal Ions, Editing Trna Synthetase, Double-Sieve, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. F. Silvian, J. Wang, T. A. Steitz
Insights Into Editing From An Ile-Trna Synthetase Structure With Trnaile And Mupirocin.
Science V. 285 1074 1999
PubMed-ID: 10446055 | Reference-DOI: 10.1126/SCIENCE.285.5430.1074
(for further references see the PDB file header)

Molecule 1 - ISOLEUCYL-TRNA
	Chains	:	T
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

Molecule 2 - ISOLEUCYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	ISOLEUCINE--TRNA LIGASE, ILERS

		1	2
Asymmetric/Biological Unit	:	A	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 14)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	MG	10	Ligand/Ion	MAGNESIUM ION
3	MRC	1	Ligand/Ion	MUPIROCIN
4	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	C T:32 , U T:33 , U T:36 , A T:38 , HOH T:1267	BINDING SITE FOR RESIDUE K T 301
02	AC2	SOFTWARE	CYS A:886 , CYS A:889 , CYS A:906 , CYS A:909	BINDING SITE FOR RESIDUE ZN A 1001
03	AC3	SOFTWARE	ASP A:13 , HIS A:201 , HIS A:770 , HOH A:2070	BINDING SITE FOR RESIDUE ZN A 1992
04	AC4	SOFTWARE	HOH T:1292 , HOH T:1293 , HOH T:1294 , HOH T:1295 , HOH T:1296 , HOH T:1297	BINDING SITE FOR RESIDUE MG T 1201
05	AC5	SOFTWARE	HOH T:1298 , HOH T:1299 , HOH T:1300 , HOH T:1301 , HOH T:1302 , HOH T:1303	BINDING SITE FOR RESIDUE MG T 1202
06	AC6	SOFTWARE	HOH A:2198 , A T:14 , HOH T:1304 , HOH T:1305 , HOH T:1306 , HOH T:1307	BINDING SITE FOR RESIDUE MG T 1203
07	AC7	SOFTWARE	G T:26 , G T:43 , A T:44 , HOH T:1218 , HOH T:1308 , HOH T:1309 , HOH T:1310 , HOH T:1311	BINDING SITE FOR RESIDUE MG T 1204
08	AC8	SOFTWARE	ASN A:713 , ASN A:718 , HOH A:2199 , C T:25 , HOH T:1312 , HOH T:1313 , HOH T:1314	BINDING SITE FOR RESIDUE MG T 1205
09	AC9	SOFTWARE	U T:8 , A T:9 , HOH T:1315 , HOH T:1316 , HOH T:1317 , HOH T:1318	BINDING SITE FOR RESIDUE MG T 1206
10	BC1	SOFTWARE	G T:16 , G T:19 , G T:59 , U T:60 , HOH T:1250 , HOH T:1319 , HOH T:1320	BINDING SITE FOR RESIDUE MG T 1207
11	BC2	SOFTWARE	ASN A:703 , HOH A:2200 , HOH A:2201 , C T:13 , A T:14 , HOH T:1321 , HOH T:1322	BINDING SITE FOR RESIDUE MG T 1208
12	BC3	SOFTWARE	U T:47 , C T:48 , G T:50 , HOH T:1323 , HOH T:1324 , HOH T:1325 , HOH T:1326	BINDING SITE FOR RESIDUE MG T 1209
13	BC4	SOFTWARE	U T:8 , U T:12 , HOH T:1318 , HOH T:1327 , HOH T:1328 , HOH T:1329 , HOH T:1330	BINDING SITE FOR RESIDUE MG T 1210
14	BC5	SOFTWARE	PRO A:56 , HIS A:64 , HIS A:67 , GLU A:554 , GLY A:555 , ASP A:557 , GLN A:558 , TRP A:562 , HIS A:585 , GLY A:586 , PHE A:587 , VAL A:588 , MET A:596 , SER A:597 , HOH A:2052 , HOH A:2085 , HOH A:2116 , HOH A:2138	BINDING SITE FOR RESIDUE MRC A 1993

(no "SS Bond" information available for 1QU2)

(no "Cis Peptide Bond" information available for 1QU2)

(no "SAP(SNP)/Variant" information available for 1QU2)

Asymmetric/Biological 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.	SYI1_STAAU	57-68	1	A:57-68

(no "Exon" information available for 1QU2)

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:917
 aligned with SYI1_STAAU | P41972 from UniProtKB/Swiss-Prot  Length:917

    Alignment length:917
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       
           SYI1_STAAU     1 MDYKETLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEYHDKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELKYGQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEYVVAQHPFLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQKYELPVISPIDDKGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRTKKPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEWVISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAKDLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPADMYLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSLGNVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDVYRKIRNTLRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFDYLNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVDMTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTFMNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALHQLFIVSQVKVVDKLDDQATAYEHGDIVIEHADGEKCERCWNYSEDLGAVDELTHLCPRCQQVVKSLV 917
               SCOP domains d1qu2a3 A:1-200,A:395-644 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                             d1qu2a2 A:201-394 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                               d1qu2a3 A:1-200,A:395-644 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                                                                               d1qu2a1 A:645-917 Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------tRNA-synt_1-1qu2A01 A:26-634                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     -------------------------------------------Anticodon_1-1qu2A03 A:678-831                                                                                                                             ---------------------------------------------------zf-FPG_IleRS-1qu2A02 A:883-912----- Pfam domains
         Sec.struct. author ..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..........hhhhhhhhhhhhhhhhhhhh.........ee...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....ee.hhh.eeeeeeeeeeee.........hhhhh......ee.hhhhh..............................hhhhhh..........................................................hhhhhh..............................hhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeeeeehhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhh..ee.ee..........ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............ee...eehhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhh.....eeeee..ee...............hhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh.eeeeee.....hhhhhhhhh.hhhhhh...eeee........eee..eeeeeee...ee......ee...eee..eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------AA_TRNA_LIGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qu2 A   1 MDYEKTLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEYHDKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELKYGQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEWVVAQHPFLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQQYELPVISPIDDKGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRTKKPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEWVISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAKDLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPADMYLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSLGNVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDDYRKIRNTLRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFDYLNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVDMTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTFMNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALHQLFIVSQVKVVDKLDDQATAYEHGDIVIEHADGEKCERCWNYSEDLGAVDELTHLCPRCQQVVKSLV 917
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910

Chain T from PDB  Type:RNA  Length:75
                                                                                                           
                 1qu2 T   1 GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC  74
                                    10        20 |      29        39        49        59        69     
                                               21A

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 1QU2)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1 (17)

Staphylococcus aureus (2)

tRNA-synt_1-1qu2A01

A:26-634

Clan: Zn_Beta_Ribbon (109)

Family: zf-FPG_IleRS (20)

Staphylococcus aureus (1)

zf-FPG_IleRS-1qu2A02

A:883-912

Clan: no clan defined [family: Anticodon_1] (10)

Family: Anticodon_1 (10)

Staphylococcus aureus (2)

Anticodon_1-1qu2A03

A:678-831

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYI1_STAAU | P41972)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0002161	aminoacyl-tRNA editing activity	The hydrolysis of an incorrectly aminoacylated tRNA.
	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:0004822	isoleucine-tRNA ligase activity	Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H(+).
	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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006428	isoleucyl-tRNA aminoacylation	The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-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:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qu2)

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	1qu2
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(no "Related Entries Specified in the PDB File" available for 1QU2)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (1, 1)

Exons (0, 0)

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