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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMOMERS, AN O-METHYL TYROSYL-TRNA SYNTHETASE EVOLVED FROM METHANOSARCINA MAZEI PYLRS, COMPLEXED WITH O-METHYL TYROSINE AND AMP-PNP
 
Authors :  N. Dellas, J. K. Takimoto, J. P. Noel, L. Wang
Date :  22 Feb 11  (Deposition) - 25 May 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pyrrolysyl-Trna Synthetase, Aminoacyl-Trna Synthetase, Atp Binding, O-Methyl Tyrosine Binding, Magnesium Binding, Aminoacylation, Esterification, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. K. Takimoto, N. Dellas, J. P. Noel, L. Wang
Stereochemical Basis For Engineered Pyrrolysyl-Trna Synthetase And The Efficient In Vivo Incorporation Of Structurally Divergent Non-Native Amino Acids.
Acs Chem. Biol. V. 6 733 2011
PubMed-ID: 21545173  |  Reference-DOI: 10.1021/CB200057A

(-) Compounds

Molecule 1 - PYRROLYSYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.26
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN OF PYLRS, UNP RESIDUES 185-454
    GeneMM_1445, PYLS
    MutationYES
    Organism CommonMETHANOSARCINA FRISIA
    Organism ScientificMETHANOSARCINA MAZEI
    Organism Taxid2209
    SynonymPYRROLYSINE-TRNA LIGASE, 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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
10A11Ligand/IonO-METHYL-L-TYROSINE
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3EDO5Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
10A12Ligand/IonO-METHYL-L-TYROSINE
2ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3EDO10Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:487 , HOH A:490 , HOH A:492 , HOH A:494 , ANP A:810BINDING SITE FOR RESIDUE MG A 800
2AC2SOFTWAREGLU A:396 , SER A:399 , HOH A:498 , HOH A:521 , ANP A:810BINDING SITE FOR RESIDUE MG A 801
3AC3SOFTWAREHOH A:70 , MET A:300 , THR A:302 , TRP A:348 , SER A:399 , LEU A:401 , GLY A:419 , ALA A:420 , HOH A:545 , EDO A:812BINDING SITE FOR RESIDUE 0A1 A 811
4AC4SOFTWARETHR A:302 , TYR A:306 , LEU A:401 , TRP A:417 , HOH A:512 , 0A1 A:811BINDING SITE FOR RESIDUE EDO A 812
5AC5SOFTWARELYS A:429 , ASP A:433 , PHE A:434BINDING SITE FOR RESIDUE EDO A 813
6AC6SOFTWARETYR A:242 , LEU A:246 , GLU A:249 , LYS A:431 , HIS A:432BINDING SITE FOR RESIDUE EDO A 814
7AC7SOFTWAREHOH A:23 , ASN A:241 , ARG A:439 , ALA A:440 , ASN A:448 , GLY A:449BINDING SITE FOR RESIDUE EDO A 815
8AC8SOFTWARETYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , GLU A:444BINDING SITE FOR RESIDUE EDO A 817
9AC9SOFTWAREHOH A:1 , HOH A:6 , HOH A:79 , HOH A:130 , HOH A:138 , 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 , HOH A:487 , HOH A:490 , HOH A:492 , HOH A:494 , HOH A:498 , MG A:800 , MG A:801BINDING SITE FOR RESIDUE ANP A 810

(-) SS Bonds  (0, 0)

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

(-) 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 3QTC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QTC)

(-) 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:257
 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 ------------------------------------------------------tRNA-synt_2b-3qtcA01 A:242-378                                                                                                           ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....----...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhhh......hhhhhh.ee...eee...hhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee.------.eeeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtc A 188 PALTKSQTDRLEVLLNPKDE----SGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLTPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLVFWQMGSGCTRENLESIITDFLNHLGIDFKIVG------GDTLDVMHGDLELSSALVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 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                                                                                                                                                                   378    385                                                                     

   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 3QTC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYLS_METMA | Q8PWY12e3c 2q7e 2q7g 2q7h 2zce 2zim 2zin 2zio 3vqv 3vqw 3vqx 4bw9 4bwa 4ch3 4ch4 4ch5 4ch6 4cs2 4cs3 4cs4 4q6g 4tqd 4tqf 4zib 5k1p 5k1x

(-) Related Entries Specified in the PDB File

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