1H3E | PR0158 - JenaLib

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Title :   TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH WILD-TYPE TRNATYR(GUA) AND WITH ATP AND TYROSINOL

Authors :   S. Cusack, A. Yaremchuk, I. Kriklivyi, M. Tukalo

Date :   28 Aug 02 (Deposition) - 27 Oct 02 (Release) - 19 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Ligase, Class I Aminoacyl-Trna Synthetase: Atp + L-Tyrosine + Trna(Tyr) -> Amp + Ppi + L-Tyrosyl-Trna(Tyr) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Yaremchuk, I. Kriklivyi, M. Tukalo, S. Cusack
Class I Tyrosyl-Trna Synthetase Has A Class Ii Mode Or Trna Recognition
Embo J. V. 21 3829 2002
PubMed-ID: 12110594 | Reference-DOI: 10.1093/EMBOJ/CDF373

Molecule 1 - TYROSYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET29B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Strain	:	HB27
	Synonym	:	TYROSINE--TRNA LIGASE

Molecule 2 - WILD-TYPE TRNATYR(GUA)
	Chains	:	B
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	1MA	1	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	5MU	1	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
3	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
4	PSU	2	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
5	TYE	1	Ligand/Ion	4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL

Biological Unit 1 (5, 12)

No.	Name	Count	Type	Full Name
1	1MA	2	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
3	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
4	PSU	4	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
5	TYE	2	Ligand/Ion	4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:43 , ALA A:44 , ASP A:45 , HIS A:52 , GLY A:54 , HIS A:55 , VAL A:58 , ARG A:93 , GLY A:193 , GLY A:194 , GLN A:197 , PRO A:222 , LEU A:223 , LEU A:224 , LYS A:232 , MET A:233 , SER A:234 , LYS A:235 , TYE A:1434	BINDING SITE FOR RESIDUE ATP A1433
2	AC2	SOFTWARE	LYS A:41 , GLY A:43 , ASP A:45 , ASP A:85 , TYR A:175 , GLN A:179 , ASP A:182 , GLU A:191 , GLN A:197 , ATP A:1433	BINDING SITE FOR RESIDUE TYE A1434

(no "SS Bond" information available for 1H3E)

Asymmetric Unit

No.	Residues
1	Val A:23	-	Pro A:24

(no "SAP(SNP)/Variant" information available for 1H3E)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S4	PS50889	S4 RNA-binding domain profile.	SYY_THET2	369-430	1	A:369-430

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S4	PS50889	S4 RNA-binding domain profile.	SYY_THET2	369-430	2	A:369-430

(no "Exon" information available for 1H3E)

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:427
 aligned with SYY_THET2 | P83453 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:427
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       
            SYY_THET2     6 HTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
               SCOP domains d1h3ea1 A:6-351 Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                                           d1h3ea2 A:352-432 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain              SCOP domains
               CATH domains --1h3eA01 A:8-223 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                   1h3eA02 A:224-340 Tyrosyl-Transfer RNA Synthetase                                                                    -----1h3eA03 A:346-421                                                           ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeehhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhh...eeeeee..hhhhhh............hhhhhhhhhhhhhhhhh.........eeeeehhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeeee........................hhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh..hhhhh.........hhhhhhhhhhhhhhh.......eeeehhhhh....eehhhhhhhh....hhhhhhhhhhh..eee..ee......ee.....eeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S4  PDB: A:369-430 UniProt: 369-430                           -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3e A   6 HTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425

Chain B from PDB  Type:DNA/RNA  Length:84
                                                                                                                    
                 1h3e B   1 GGGCAGGUUCCCGAGCGGCCAAAGGGGACGGUCUGuAAAACCGUUGGCGUAUGCCUUCGCUGGuuCGaAUCCAGCCCUGCCCAC  74
                                    10     ||20A|       29     |  39       47B||||||| 50   ||  |60        70    
                                          16|  ||             35-PSU      47A||||||||     54-5MU                
                                           18  ||                          47B|||||||      55-PSU               
                                             20A|                           47C||||||         58-1MA            
                                              20B                            47D|||||                           
                                                                              47E||||                           
                                                                               47F|||                           
                                                                                47G||                           
                                                                                 47H|                           
                                                                                  47I

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 "Pfam Domain" information available for 1H3E)

Asymmetric Unit(hide GO term definitions)

Chain A (SYY_THET2 | P83453)

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:0004831	tyrosine-tRNA ligase activity	Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
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:0006437	tyrosyl-tRNA aminoacylation	The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-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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	Ligands, Modified Residues, Ions
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		5MU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PSU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TYE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:23 - Pro A:24	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1h3e
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	6.1.1.1
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	SYY_THET2 \| P83453	:	1h3f

1h3f	TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TYROSINOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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