2Q7G - JenaLib

Title :   PYRROLYSINE TRNA SYNTHETASE BOUND TO A PYRROLYSINE ANALOGUE (CYC) AND ATP

Authors :   J. M. Kavran, T. A. Steitz

Date :   06 Jun 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Pyrrolysyl-Trna Syntethetase, Pyrrolysine, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Kavran, S. Gundllapalli, P. O'Donoghue, M. Englert, D. Soll, T. A. Steitz
Structure Of Pyrrolysyl-Trna Synthetase, An Archaeal Enzyme For Genetic Code Innovation.
Proc. Natl. Acad. Sci. Usa V. 104 11268 2007
PubMed-ID: 17592110 | Reference-DOI: 10.1073/PNAS.0704769104

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ATP A:900 , HOH A:996 , HOH A:998 , HOH A:1087 , HOH A:1088	BINDING SITE FOR RESIDUE MG A 500
02	AC2	SOFTWARE	GLU A:396 , SER A:399 , ATP A:900 , HOH A:1125 , HOH A:1158	BINDING SITE FOR RESIDUE MG A 501
03	AC3	SOFTWARE	ARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , MET A:344 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , GLY A:421 , GLY A:423 , ARG A:426 , MG A:500 , MG A:501 , CCL A:901 , EDO A:906 , HOH A:912 , HOH A:996 , HOH A:998 , HOH A:1087 , HOH A:1088 , HOH A:1125 , HOH A:1126 , HOH A:1128 , HOH A:1158 , HOH A:1160	BINDING SITE FOR RESIDUE ATP A 900
04	AC4	SOFTWARE	ASN A:241 , ARG A:439 , ALA A:440 , ASN A:448 , GLY A:449 , HOH A:960	BINDING SITE FOR RESIDUE EDO A 902
05	AC5	SOFTWARE	TYR A:242 , LEU A:246 , GLU A:249 , LYS A:431 , HIS A:432	BINDING SITE FOR RESIDUE EDO A 903
06	AC6	SOFTWARE	ASP A:373 , HIS A:392 , GLY A:393 , EDO A:904	BINDING SITE FOR RESIDUE EDO A 907
07	AC7	SOFTWARE	TYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , GLU A:444 , HOH A:983	BINDING SITE FOR RESIDUE EDO A 908
08	AC8	SOFTWARE	ASP A:373 , LYS A:375 , MET A:391 , HIS A:392 , GLY A:393 , EDO A:907	BINDING SITE FOR RESIDUE EDO A 904
09	AC9	SOFTWARE	SER A:225 , EDO A:910 , HOH A:975 , HOH A:980	BINDING SITE FOR RESIDUE EDO A 909
10	BC1	SOFTWARE	SER A:221 , LYS A:228 , EDO A:909	BINDING SITE FOR RESIDUE EDO A 910
11	BC2	SOFTWARE	ARG A:310 , ASP A:313 , GLY A:412 , ILE A:413 , ASP A:414 , LYS A:415	BINDING SITE FOR RESIDUE EDO A 905
12	BC3	SOFTWARE	LEU A:339 , GLU A:340 , GLU A:341 , ALA A:441 , HOH A:988	BINDING SITE FOR RESIDUE EDO A 911
13	BC4	SOFTWARE	GLU A:337 , HIS A:338 , ASP A:394 , GLU A:396 , ATP A:900	BINDING SITE FOR RESIDUE EDO A 906
14	BC5	SOFTWARE	ALA A:302 , LEU A:305 , TYR A:306 , ASN A:346 , SER A:399 , TRP A:417 , GLY A:419 , ALA A:420 , GLY A:421 , ATP A:900 , HOH A:1155 , HOH A:1157	BINDING SITE FOR RESIDUE CCL A 901

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:250
 aligned with PYLS_METMA | Q8PWY1 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:267
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       
           PYLS_METMA   188 PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 454
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q7gA01 A:188-239 He      lix hairpin bin           2q7gA02 A:240-454 Bira Bifunctional Prot    ein; Domain 2                                                                                                                                                               CATH domains
               Pfam domains --------------------      ----------------------------tRNA-synt_2b-2q7gA01 A:242-378                                                                                                                  --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....------.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhhh...----hhhhh.ee...eee...hhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee.-------.eeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7g A 188 PALTKSQTDRLEVLLNPKDE------KPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGID----LSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVG-------DTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 454
                                   197       207      |217       227       237       247       257       267       277 |    |287       297       307       317       327       337       347       357       367       377|      387       397       407       417       427       437       447       
                                             207    214                                                              279  284                                                                                           378     386

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (PYLS_METMA | Q8PWY1)

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: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: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.

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	Cis Peptide Bonds
		Asp A:318 - Pro A:319	[ RasMol ]
		Gly A:403 - Pro A:404	[ RasMol ]
		Lys A:214 - Pro A:215	[ RasMol ]

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