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(-) Description

Title :  STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED PROPIONYL LYSINE
 
Authors :  V. Fluegel, M. Vrabel, S. Schneider
Date :  28 Nov 13  (Deposition) - 19 Mar 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Non-Natural Amino Acid, Pyrrolysine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Flugel, M. Vrabel, S. Schneider
Structural Basis For The Site-Specific Incorporation Of Lysine Derivatives Into Proteins.
Plos One V. 9E96198 2014
PubMed-ID: 24760130  |  Reference-DOI: 10.1371/JOURNAL.PONE.0096198

(-) Compounds

Molecule 1 - PYRROLYSINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 185-454
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 192952
    Strain: GO1
    Synonym: PYRROLYSINE--TRNA(PYL) LIGASE, PYRROLYSYL-TRNA SYNTHETASE, PYLRS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-
4YLP1Ligand/Ion(S)-2-AMINO-6-PROPIONAMIDOHEXANOIC(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC)ANHYDRIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , MET A:344 , ASN A:346 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , TRP A:417 , GLY A:421 , GLY A:423 , ARG A:426 , MG A:1455 , POP A:1461 , HOH A:2047 , HOH A:2081BINDING SITE FOR RESIDUE YLP A 500
2AC2SOFTWAREGLU A:396 , SER A:399 , YLP A:500 , POP A:1461BINDING SITE FOR RESIDUE MG A1455
3AC3SOFTWARETYR A:242 , LYS A:245 , GLU A:249 , LYS A:431 , HIS A:432BINDING SITE FOR RESIDUE EDO A1456
4AC4SOFTWAREASP A:313 , GLY A:412 , ASP A:414 , LYS A:415 , HOH A:2049BINDING SITE FOR RESIDUE EDO A1457
5AC5SOFTWAREASN A:241 , ARG A:439 , ALA A:440 , ALA A:441 , ASN A:448 , GLY A:449 , HOH A:2083BINDING SITE FOR RESIDUE EDO A1458
6AC6SOFTWARETYR A:272 , ASN A:307 , ARG A:310 , LYS A:311BINDING SITE FOR RESIDUE EDO A1459
7AC7SOFTWAREASP A:373 , LYS A:375 , GLY A:393BINDING SITE FOR RESIDUE EDO A1460
8AC8SOFTWAREARG A:330 , GLU A:332 , HIS A:338 , GLU A:396 , ARG A:426 , YLP A:500 , MG A:1455BINDING SITE FOR RESIDUE POP A1461

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CH5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 4CH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CH5)

(-) Exons   (0, 0)

(no "Exon" information available for 4CH5)

(-) Sequences/Alignments

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:263
 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.......eee...hhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee..----...eeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ch5 A 188 PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGD----YGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 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       
                                                                                                                                                                                                                         379  384
   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)

(no "SCOP Domain" information available for 4CH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CH5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological 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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 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 3vqv 3vqw 3vqx 4bw9 4bwa 4ch3 4ch4 4ch6 4cs2 4cs3 4cs4 4q6g 4tqd 4tqf 4zib 5k1p 5k1x

(-) Related Entries Specified in the PDB File

4ch3 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED BUTYRYL LYSINE
4ch4 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED CROTONYL LYSINE
4ch6 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED PROPARGYLOXYCARBONYL LYSINE