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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH AMPPNP (RE-REFINED)
 
Authors :  T. Yanagisawa, T. Sumida, R. Ishii, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  01 Apr 12  (Deposition) - 02 Jan 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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, 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
(for further references see the PDB file header)

(-) 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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 , MG A:502 , MG A:503 , HOH A:601 , HOH A:602 , HOH A:657 , HOH A:678 , HOH A:752 , HOH A:768 , HOH A:772 , HOH A:779 , HOH A:792 , HOH A:809 , HOH A:813 , HOH A:822BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWAREANP A:501 , HOH A:752 , HOH A:768 , HOH A:772 , HOH A:779BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREGLU A:396 , SER A:399 , ANP A:501 , HOH A:813BINDING SITE FOR RESIDUE MG A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VQV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VQV)

(-) Exons   (0, 0)

(no "Exon" information available for 3VQV)

(-) 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:258
 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....----...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhhh......hhhhhh.ee...eee...hhhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee..-----..eeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqv A 188 PALTKSQTDRLEVLLNPKDE----SGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGD-----GDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL 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  212                                                                                                                                                                    379   385
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 2ZCD: 2,2)

(no "CATH Domain" information available for 3VQV, only for superseded entry 2ZCD replaced by 3VQV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VQV)

(-) Gene Ontology  (9, 9)

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: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 and the alpha carboxylic acid group of an amino acid, 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 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.

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  3vqv
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  PYLS_METMA | Q8PWY1
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  6.1.1.26
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYLS_METMA | Q8PWY1: 2e3c 2q7e 2q7g 2q7h 2zce 2zim 2zin 2zio 3qtc 3vqw 3vqx 4bw9 4bwa 4ch3 4ch4 4ch5 4ch6 4cs2 4cs3 4cs4 4q6g 4tqd 4tqf 4zib 5k1p 5k1x

(-) Related Entries Specified in the PDB File

2e3c
2zcd
2zce
2zin
2zio
3vqw
3vqx
3vqy RELATED ID: RSGI-TRT001000322.1 RELATED DB: TARGETTRACK