2CSX | PR0161 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS METHIONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(MET)

Authors :   K. Nakanishi, Y. Ogiso, T. Nakama, S. Fukai, O. Nureki, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   23 May 05 (Deposition) - 20 Sep 05 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Ligase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Nakanishi, Y. Ogiso, T. Nakama, S. Fukai, O. Nureki
Structural Basis For Anticodon Recognition By Methionyl-Trna Synthetase.
Nat. Struct. Mol. Biol. V. 12 931 2005
PubMed-ID: 16155581 | Reference-DOI: 10.1038/NSMB988
(for further references see the PDB file header)

Molecule 1 - RNA (75-MER)
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - METHIONYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 CODON+ (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	METHIONINE--TRNA LIGASE, METRS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2CSX)

(no "Site" information available for 2CSX)

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

(no "Cis Peptide Bond" information available for 2CSX)

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

(no "PROSITE Motif" information available for 2CSX)

(no "Exon" information available for 2CSX)

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:464
 aligned with SYM_AQUAE | O67298 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:497
                                    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       
            SYM_AQUAE     1 MTLMKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRDYDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECYKRGDIYLGEYEGWYCVGCEEFKSEAELAEDHTCPIHQKKCEYIKEPSYFFRLSKYQDKLLELYEKNPEFIQPDYRRNEIISFVKQGLKDLSVTRPRSRVKWGIPVPFDPEHTIYVWFDALFNYISALEDKVEIYWPADLHLVGKDILRFHTVYWPAFLMSLGYELPKKVFAHGWWTVEGKKMSKTLGNVVDPYEVVQEYGLDEVRYFLLREVPFGQDGDFSKKAILNRINGELANEIGNLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYENYMEKVNFYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKVLYALVDGLFVLTHLLYPITPNKMKEALQMLGEKEFLKELKPYSKNTYKLGERKILFPKREG 497
               SCOP domains d2csxa1 A:1-346 automated matches                                                                                                                                                                                                                                                                                                                         d2csxa2 A:347-497 automated matches                                                                                                                     SCOP domains
               CATH domains 2csxA01 A:1-117,A:229-334 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                      ---------------------------------------------------------------------------------------------------------------2csxA01 A:1-117,A:229-334 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeee.---------------------------------..eeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...ee.eee.......eee..eeeeee.hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh......eeee..ee..............hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2csx A   1 MTLMKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRDYDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECYKRGDIYLGEY---------------------------------KEPSYFFRLSKYQDKLLELYEKNPEFIQPDYRRNEIISFVKQGLKDLSVTRPRSRVKWGIPVPFDPEHTIYVWFDALFNYISALEDKVEIYWPADLHLVGKDILRFHTVYWPAFLMSLGYELPKKVFAHGWWTVEGKKMSKTLGNVVDPYEVVQEYGLDEVRYFLLREVPFGQDGDFSKKAILNRINGELANEIGNLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYENYMEKVNFYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKVLYALVDGLFVLTHLLYPITPNKMKEALQMLGEKEFLKELKPYSKNTYKLGERKILFPKREG 497
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     -         -         -       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       
                                                                                                                                                     124                               158

Chain B from PDB  Type:PROTEIN  Length:464
 aligned with SYM_AQUAE | O67298 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:497
                                    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       
            SYM_AQUAE     1 MTLMKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRDYDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECYKRGDIYLGEYEGWYCVGCEEFKSEAELAEDHTCPIHQKKCEYIKEPSYFFRLSKYQDKLLELYEKNPEFIQPDYRRNEIISFVKQGLKDLSVTRPRSRVKWGIPVPFDPEHTIYVWFDALFNYISALEDKVEIYWPADLHLVGKDILRFHTVYWPAFLMSLGYELPKKVFAHGWWTVEGKKMSKTLGNVVDPYEVVQEYGLDEVRYFLLREVPFGQDGDFSKKAILNRINGELANEIGNLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYENYMEKVNFYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKVLYALVDGLFVLTHLLYPITPNKMKEALQMLGEKEFLKELKPYSKNTYKLGERKILFPKREG 497
               SCOP domains d2csxb1 B:1-346 automated matches                                                                                                                                                                                                                                                                                                                         d2csxb2 B:347-497 automated matches                                                                                                                     SCOP domains
               CATH domains 2csxB01 B:1-117,B:229-334 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                      ---------------------------------------------------------------------------------------------------------------2csxB01 B:1-117,B:229-334 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeee.---------------------------------..eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee..ee.......eee..eeeeee.hhhhhhhhhhhh...hhhhhh....eeee..hhhhhhhhhhhhhhhhh......eeee..ee..............hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...............ee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2csx B   1 MTLMKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRDYDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECYKRGDIYLGEY---------------------------------KEPSYFFRLSKYQDKLLELYEKNPEFIQPDYRRNEIISFVKQGLKDLSVTRPRSRVKWGIPVPFDPEHTIYVWFDALFNYISALEDKVEIYWPADLHLVGKDILRFHTVYWPAFLMSLGYELPKKVFAHGWWTVEGKKMSKTLGNVVDPYEVVQEYGLDEVRYFLLREVPFGQDGDFSKKAILNRINGELANEIGNLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYENYMEKVNFYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKVLYALVDGLFVLTHLLYPITPNKMKEALQMLGEKEFLKELKPYSKNTYKLGERKILFPKREG 497
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     -         -         -       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       
                                                                                                                                                     124                               158

Chain C from PDB  Type:RNA  Length:75
                                                                                                           
                 2csx C   1 GGCGGCGUAGCUCAGCUGGUCAGAGCGGGGAUCUCAUAAGUCCCAGGUCGGAGGUUCGAGUCCUCCCGCCGCCAC  74
                                    10        20 |      29        39        49        59        69     
                                               21A

Chain D from PDB  Type:RNA  Length:75
                                                                                                           
                 2csx D   1 GGCGGCGUAGCUCAGCUGGUCAGAGCGGGGAUCUCAUAAGUCCCAGGUCGGAGGUUCGAGUCCUCCCGCCGCCAC  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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

[unclassified] (27)

1a	2csxA01	A:1-117,A:229-334
1b	2csxB01	B:1-117,B:229-334

(no "Pfam Domain" information available for 2CSX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYM_AQUAE | O67298)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004825	methionine-tRNA ligase activity	Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
	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.
biological process
	GO:0006431	methionyl-tRNA aminoacylation	The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
	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 and the alpha carboxylic acid group of an amino acid, 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 Unit
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	SYM_AQUAE \| O67298	:	2ct8

2ct8	THE SAME PROTEIN COMPLEXED WITH TRNA(MET) AND METHIONYL- ADENYLATE ANOLOGUE RELATED ID: AAE001001257.1 RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (0, 0)

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