3AFH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA NONDISCRIMINATING GLUTAMYL-TRNA SYNTHETASE IN COMPLEX WITH A GLUTAMYL-AMP ANALOG

Authors :   T. Ito, S. Yokoyama

Date :   01 Mar 10 (Deposition) - 30 Jun 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Protein-Substrate Complex, Non-Discriminating Glutamyl-Trna Synthetase, Aminoacyl-Trna Synthetase, Atp-Binding, Ligase, Nucleotide-Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ito, N. Kiyasu, R. Matsunaga, S. Takahashi, S. Yokoyama
Structure Of Nondiscriminating Glutamyl-Trna Synthetase Fro Thermotoga Maritima
Acta Crystallogr. , Sect. D V. 66 813 2010
PubMed-ID: 20606262 | Reference-DOI: 10.1107/S0907444910019086

Molecule 1 - GLUTAMYL-TRNA SYNTHETASE 2
	Chains	:	A
	EC Number	:	6.1.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Vector	:	VECTOR
	Expression System Vector Type	:	PET-28B(+)
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	GLUTAMATE--TRNA LIGASE 2, GLURS 2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GSU	1	Ligand/Ion	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:28 , ALA A:30 , PRO A:31 , SER A:32 , GLY A:40 , GLY A:41 , THR A:44 , GLU A:64 , ARG A:216 , GLY A:217 , ASP A:219 , HIS A:220 , LEU A:246 , ILE A:247 , HOH A:1004 , HOH A:1005 , HOH A:1011 , HOH A:1141 , HOH A:1143 , HOH A:1222 , HOH A:1227 , HOH A:1351	BINDING SITE FOR RESIDUE GSU A 2001

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:101	-	Pro A:102

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

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.	SYE2_THEMA	31-42	1	A:31-42

(no "Exon" information available for 3AFH)

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:463
 aligned with SYE2_THEMA | Q9X2I8 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:463
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483   
           SYE2_THEMA    24 LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESLRWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKEDPSKELFTTYEYPHEYKEKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIPLILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGDEIFTIEEKLQSFDPKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNMEEIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERTLKRLERTLQFLKK 486
               SCOP domains d3afha1 A:24-315 automated matches                                                                                                                                                                                                                                                                  d3afha2 A:316-486 automated matches                                                                                                                                         SCOP domains
               CATH domains 3afhA01 A:24-93,A:198-248                                             3afhA02 A:94-197 Glutamyl-tRNA Synthetase; Domain 3                                                     3afhA01 A:24-93,A:198-248                          3afhA03 A:249-331 Glutamyl-trna Synthetase; Domain 2                               ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh..eeeeee.......eeeee...hhhhhhh...eeeee.....eeeeee...eeeeee.hhh..eeee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..ee..............hhhhhhhhh.hhhhhhhhhhhh..........hhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afh A  24 LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESLRWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKEDPSKELFTTYEYPHEYKEKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIPLILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGDEIFTIEEKLQSFDPKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNMEEIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERTLKRLERTLQFLKK 486
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483

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 3AFH)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYE2_THEMA | Q9X2I8)

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:0004818	glutamate-tRNA ligase activity	Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
	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:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	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:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006424	glutamyl-tRNA aminoacylation	The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-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:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	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.
	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/Biological Unit
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	Cis Peptide Bonds
		Gly A:101 - Pro A:102	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3AFH)

Description

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Chains, Units

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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