3QE4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   AN EVOLVED AMINOACYL-TRNA SYNTHETASE WITH ATYPICAL POLYSUBSTRATE SPECIFICITY

Authors :   D. D. Young, T. S. Young, M. Jahnz, I. Ahmad, G. Spraggon, P. G. Schultz

Date :   19 Jan 11 (Deposition) - 16 Feb 11 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Evolved Trna Synthetase, Trna Synthetase Evolved To Bind Unnatural Amino Acids, Trna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. D. Young, T. S. Young, M. Jahnz, I. Ahmad, G. Spraggon, P. G. Schultz
An Evolved Aminoacyl-Trna Synthetase With Atypical Polysubstrate Specificity .
Biochemistry V. 50 1894 2011
PubMed-ID: 21280675 | Reference-DOI: 10.1021/BI101929E

Molecule 1 - TYROSYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET101
	Gene	:	MJ0389, TYRRS, TYRS
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	TYROSINE--TRNA LIGASE, TYRRS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	4CF	2	Ligand/Ion	4-CYANO-L-PHENYLALANINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	4CF	1	Ligand/Ion	4-CYANO-L-PHENYLALANINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	4CF	1	Ligand/Ion	4-CYANO-L-PHENYLALANINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:34 , PHE A:35 , ALA A:67 , HIS A:70 , TYR A:151 , GLN A:155 , GLY A:158 , GLN A:173 , HOH A:339 , HOH A:370	BINDING SITE FOR RESIDUE 4CF A 313
2	AC2	SOFTWARE	GLY B:34 , PHE B:35 , GLU B:36 , ALA B:67 , HIS B:70 , TYR B:151 , GLN B:155 , GLY B:158 , GLN B:173	BINDING SITE FOR RESIDUE 4CF B 313

(no "SS Bond" information available for 3QE4)

Asymmetric Unit

No.	Residues
1	Met A:1	-	Asp A:2
2	Ile A:15	-	Ser A:16
3	Tyr A:251	-	Pro A:252
4	Ile B:15	-	Ser B:16
5	Tyr B:251	-	Pro B:252

(no "SAP(SNP)/Variant" information available for 3QE4)

Asymmetric Unit (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.	SYY_METJA	37-46	2	A:37-46 B:37-46

Biological Unit 1 (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.	SYY_METJA	37-46	1	A:37-46 -

Biological Unit 2 (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.	SYY_METJA	37-46	1	- B:37-46

(no "Exon" information available for 3QE4)

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:307
 aligned with SYY_METJA | Q57834 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:307
                                                                                                                                                                                                                                                                                                                                           306 
                                    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     | 
            SYY_METJA     1 MDEFEMIKRNTSEIISEEELREVLKKDEKSAYIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNDIHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh...hhhhhhhhhhhhhhhhh......eeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhhh.........hhhhhhhhhhh...eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qe4 A   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIVLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEWMLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNGAHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLL 307
                                    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

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with SYY_METJA | Q57834 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:306
                                                                                                                                                                                                                                                                                                                                          306 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    | 
            SYY_METJA     2 DEFEMIKRNTSEIISEEELREVLKKDEKSAYIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNDIHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------tRNA-synt_1b-3qe4B01 B:24-300                                                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ----------------------tRNA-synt_1b-3qe4B02 B:24-300                                                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author .hhhhhhh...eeehhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhhh.........hhhhhhhhhhh...eeee.hhhhh.eeee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qe4 B   2 DEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIVLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEWMLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNGAHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLL 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

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 "SCOP Domain" information available for 3QE4)

(no "CATH Domain" information available for 3QE4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (7)

1a	tRNA-synt_1b-3qe4B01	B:24-300
1b	tRNA-synt_1b-3qe4B02	B:24-300

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYY_METJA | Q57834)

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:0004831	tyrosine-tRNA ligase activity	Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
	GO:0004832	valine-tRNA ligase activity	Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + 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.
	GO:0006438	valyl-tRNA aminoacylation	The process of coupling valine to valyl-tRNA, catalyzed by valyl-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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
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		Met A:1 - Asp A:2	[ RasMol ]
		Tyr A:251 - Pro A:252	[ RasMol ]
		Tyr B:251 - Pro B:252	[ RasMol ]

Biological Units
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	3qe4
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	SYY_METJA \| Q57834
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (12, 12)

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