3VQY - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH BOCLYS AND AMPPNP (FORM 2)

Authors :   T. Yanagisawa, T. Sumida, R. Ishii, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   02 Apr 12 (Deposition) - 02 Jan 13 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Aminoacyl-Trna Synthetase, Pyrrolysyl-Trna Synthetase, Amppnp, Boclys, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yanagisawa, T. Sumida, R. Ishii, S. Yokoyama
A Novel Crystal Form Of Pyrrolysyl-Trna Synthetase Reveals The Pre- And Post-Aminoacyl-Trna Synthesis Conformational States Of The Adenylate And Aminoacyl Moieties And An Asparagine Residue In The Catalytic Site
Acta Crystallogr. , Sect. D V. 69 5 2013
PubMed-ID: 23275158 | Reference-DOI: 10.1107/S0907444912039881

Compounds

Molecule 1 - PYRROLYSINE--TRNA LIGASE
	Chains	:	A
	EC Number	:	6.1.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28C
	Expression System Strain	:	BL21(DE3) CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYLS
	Mutation	:	YES
	Organism Scientific	:	METHANOSARCINA MAZEI
	Organism Taxid	:	2209
	Strain	:	JCM9314
	Synonym	:	PYRROLYSYL-TRNA SYNTHETASE, PYLRS

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	LBY	1	Ligand/Ion	N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	LBY	2	Ligand/Ion	N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	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 , LBY A:502 , MG A:503 , MG A:504 , HOH A:602 , HOH A:640 , HOH A:656 , HOH A:670 , HOH A:685 , HOH A:697	BINDING SITE FOR RESIDUE ANP A 501
2	AC2	SOFTWARE	MET A:276 , ALA A:302 , TYR A:306 , ASN A:346 , SER A:399 , ILE A:405 , TRP A:417 , ALA A:420 , GLY A:421 , ANP A:501	BINDING SITE FOR RESIDUE LBY A 502
3	AC3	SOFTWARE	ARG A:330 , ANP A:501 , HOH A:601 , HOH A:656 , HOH A:685 , HOH A:697	BINDING SITE FOR RESIDUE MG A 503
4	AC4	SOFTWARE	GLU A:396 , SER A:399 , ANP A:501 , HOH A:640	BINDING SITE FOR RESIDUE MG A 504

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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

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Chain A from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhhh......hhhhh..ee...eee...hhhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee..eeeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhh.....ee..ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqy A 188 PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL 454
                                   197       207|      221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      |387       397       407       417       427       437       447       
                                             207|                                                                                                                                                                   378|                                                                     
                                              212                                                                                                                                                                    385

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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