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(-) Description

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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2LBY1Ligand/IonN~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2LBY2Ligand/IonN~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG 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:697BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWAREMET 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:501BINDING SITE FOR RESIDUE LBY A 502
3AC3SOFTWAREARG A:330 , ANP A:501 , HOH A:601 , HOH A:656 , HOH A:685 , HOH A:697BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREGLU A:396 , SER A:399 , ANP A:501 , HOH A:640BINDING SITE FOR RESIDUE MG A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:318 -Pro A:319
2Gly A:403 -Pro A:404

 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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: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)

(no "SCOP Domain" information available for 3VQY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VQY)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  6.1.1.26
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3VQY)

(-) Related Entries Specified in the PDB File

2e3c
2zcd
2zce
2zin
2zio
3vqv
3vqw
3vqx RELATED ID: RSGI-TRT001000322.8 RELATED DB: TARGETTRACK