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Title :   METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINYL ADENYLATE

Authors :   T. Crepin, E. Schmitt, Y. Mechulam, P. B. Sampson, M. D. Vaughan, J. F. Honek, S. Blanquet

Date :   27 May 03 (Deposition) - 17 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Rossmann Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Crepin, E. Schmitt, Y. Mechulam, P. B. Sampson, M. D. Vaughan, J. F. Honek, S. Blanquet
Use Of Analogues Of Methionine And Methionyl Adenylate To Sample Conformational Changes During Catalysis In Escherichia Coli Methionyl-Trna Synthetase.
J. Mol. Biol. V. 332 59 2003
PubMed-ID: 12946347 | Reference-DOI: 10.1016/S0022-2836(03)00917-3
(for further references see the PDB file header)

Molecule 1 - METHIONYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBLUESCRIPT
	Expression System Strain	:	JM101TR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-551
	Gene	:	METG
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	METHIONINE--TRNA LIGASE, METRS

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MOD	1	Ligand/Ion	L-METHIONYL ADENYLATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:12 , LEU A:13 , PRO A:14 , TYR A:15 , HIS A:21 , GLY A:23 , HIS A:24 , GLU A:27 , ASP A:52 , TRP A:253 , ALA A:256 , PRO A:257 , TYR A:260 , GLY A:294 , ASP A:296 , ILE A:297 , HIS A:323 , GLY A:324 , TYR A:325 , VAL A:326 , HOH A:1091 , HOH A:1187 , HOH A:1189 , HOH A:1191	BINDING SITE FOR RESIDUE MOD A 553

(no "SS Bond" information available for 1PG0)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:235	-	Pro A:236

(no "SAP(SNP)/Variant" information available for 1PG0)

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.	SYM_ECOLI	15-26	1	A:14-25

(no "Exon" information available for 1PG0)

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:492
 aligned with SYM_ECOLI | P00959 from UniProtKB/Swiss-Prot  Length:677

    Alignment length:547
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       
            SYM_ECOLI     5 AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRMRGHEVNFICADDAHGTPIMLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRLKENGFIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVVSGATPVMRDSEHFFFDLPSFSEMLQAWTRSGALQEQVANKMQEWFESGLQQWDISRDAPYFGFEIPNAPGKYFYVWLDAPIGYMGSFKNLCDKRGDSVSFDEYWKKDSTAELYHFIGKDIVYFHSLFWPAMLEGSNFRKPSNLFVHGYVTVNGAKMSKSRGTFIKASTWLNHFDADSLRYYYTAKLSSRIDDIDLNLEDFVQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWESREFGKAVREIMALADLANRYVDEQAPWVVAKQEGRDADLQAICSMGINLFRVLMTYLKPVLPKLTERAEAFLNTELTWDGIQQPLLGHKVNPFKALYNRIDMRQVEALVEASKEEV 551
               SCOP domains d1pg0a2 A:4-129,A:185-388 Methionyl-tRNA synthetase (MetRS)                                                                   -------------------------------------------------------d1pg0a2 A:4-129,A:185-388 Methionyl-tRNA synthetase (MetRS)                                                                                                                                                 d1pg0a1 A:389-550 Methionyl-tRNA synthetase (MetRS)                                                                                                                SCOP domains
               CATH domains 1pg0A01 A:4-388,A:532-550 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                                                                                  1pg0A02 A:389-531 Isoleucyl-tRNA Synthetase; Domain 1                                                                                          1pg0A01             CATH domains
               Pfam domains ---tRNA-synt_1g-1pg0A01 A:7-397                                                                                                                                                                                                                                                                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeee....-------------------------------------------------------.eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhh.....ee.eee.............eeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhh......eeeee..eee.............hhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhh.................hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LIGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pg0 A   4 AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRMRGHEVNFICADDAHGTPIMLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRLKENGFIKNRTISQLYD-------------------------------------------------------RDSEHFFFDLPSFSEMLQAWTRSGALQEQVANKMQEWFESGLQQWDISRDAPYFGFEIPNAPGKYFYVWLDAPIGYMGSFKNLCDKRGDSVSFDEYWKKDSTAELYHFIGKDIVYFHSLFWPAMLEGSNFRKPSNLFVHGYVTVNGAKMSKSRGTFIKASTWLNHFDADSLRYYYTAKLSSRIDDIDLNLEDFVQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWESREFGKAVREIMALADLANRYVDEQAPWVVAKQEGRDADLQAICSMGINLFRVLMTYLKPVLPKLTERAEAFLNTELTWDGIQQPLLGHKVNPFKALYNRIDMRQVEALVEASKEEV 550
                                    13        23        33        43        53        63        73        83        93       103       113       123     |   -         -         -         -         -         - |     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       493       503       513       523       533       543       
                                                                                                                                                       129                                                     185

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/Biological 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)

Escherichia coli. Organism_taxid: 562. (18)

1pg0A01

A:4-388,A:532-550

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Isoleucyl-tRNA Synthetase; Domain 1 (35)

Homologous Superfamily: Isoleucyl-tRNA Synthetase; Domain 1 (35)

Escherichia coli. Organism_taxid: 562. (8)

1pg0A02

A:389-531

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1g (19)

Escherichia coli (strain K12) (10)

tRNA-synt_1g-1pg0A01

A:7-397

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYM_ECOLI | P00959)

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: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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006431	methionyl-tRNA aminoacylation	The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-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: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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:235 - Pro A:236	[ RasMol ]

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	6.1.1.10
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	SYM_ECOLI \| P00959	:	1f4l 1mea 1med 1p7p 1pfu 1pfv 1pfw 1pfy 1pg2 1qqt 3h97 3h99 3h9b 3h9c

1p7p	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE
1pfu	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE
1pfv	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE
1pfw	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE
1pfy	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE
1pg2	METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONINE PHOSPHINATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

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