2PXH - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A BIPYRIDYLALANYL-TRNA SYNTHETASE

Authors :   W. Liu, J. Xie, P. G. Schultz

Date :   14 May 07 (Deposition) - 05 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

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

Keywords :   Metal Chelator, Bipyridylalanine, Unnatural Amino Acid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Xie, W. Liu, P. G. Schultz
A Genetically Encoded Bidentate, Metal-Binding Amino Acid.
Angew. Chem. Int. Ed. Engl. V. 46 9239 2007
PubMed-ID: 17893898 | Reference-DOI: 10.1002/ANIE.200703397

Molecule 1 - TYROSYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TYROSYL-TRNA SYNTHETASE
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	TYROSINE--TRNA LIGASE, TYRRS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	BP5	1	Ligand/Ion	3-(2,2'-BIPYRIDIN-5-YL)-L-ALANINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BP5	1	Ligand/Ion	3-(2,2'-BIPYRIDIN-5-YL)-L-ALANINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	BP5	2	Ligand/Ion	3-(2,2'-BIPYRIDIN-5-YL)-L-ALANINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:34 , GLU A:36 , TYR A:65 , ALA A:67 , TYR A:151 , GLU A:155 , GLY A:158 , TRP A:159 , GLN A:173 , HOH A:310 , HOH A:445 , HOH A:501 , HOH A:586	BINDING SITE FOR RESIDUE BP5 A 308

(no "SS Bond" information available for 2PXH)

Asymmetric Unit

No.	Residues
1	Tyr A:251	-	Pro A:252

(no "SAP(SNP)/Variant" information available for 2PXH)

Asymmetric 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.	SYY_METJA	37-46	1	A: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, 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

(no "Exon" information available for 2PXH)

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: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 d2pxha_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2pxhA01 A:2-196 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                              2pxhA02 A:197-307 Tyrosyl-Transfer RNA Synthetase                                                               CATH domains
               Pfam domains ----------------------tRNA-synt_1b-2pxhA01 A:24-300                                                                                                                                                                                                                                                        ------- Pfam domains
         Sec.struct. author hhhhhhhh...eeehhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee.hhh..hhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........................hhhhhhhhhhh..........hhhhhhhhhhh...eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pxh A   2 DEFEMIKRNTSEIISEEELREVLKKDEKSAGIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIIYLADLAAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMEVNGWHYSGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRLL 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain (137)

Protein domain: automated matches (22)

Methanocaldococcus jannaschii [TaxId: 2190] (7)

d2pxha_

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)

tRNA-synt_1b-2pxhA01

A:24-300

Asymmetric Unit(hide GO term definitions)

Chain A (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.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:251 - Pro A:252	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2pxh
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	SYY_METJA \| Q57834
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	6.1.1.1
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (2, 2)

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Gene Ontology (12, 12)

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