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(-) Description

Title :  PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED PYRROLYSINE AND PYROPHOSPHATE
 
Authors :  J. M. Kavran, T. A. Steitz
Date :  06 Jun 07  (Deposition) - 24 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pyrrolysyl-Trna Synthetase, Pyrrolysine, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Kavran, S. Gundllapalli, P. O'Donoghue, M. Englert, D. Soll, T. A. Steitz
Structure Of Pyrrolysyl-Trna Synthetase, An Archaeal Enzyme For Genetic Code Innovation.
Proc. Natl. Acad. Sci. Usa V. 104 11268 2007
PubMed-ID: 17592110  |  Reference-DOI: 10.1073/PNAS.0704769104

(-) Compounds

Molecule 1 - PYRROLYSYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 CODONPLUS RIL (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: PYLS
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
    Synonym: PYRROLYSINE-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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2POP1Ligand/IonPYROPHOSPHATE 2-
3YLY1Ligand/Ion(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1EDO20Ligand/Ion1,2-ETHANEDIOL
2POP2Ligand/IonPYROPHOSPHATE 2-
3YLY2Ligand/Ion(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:241 , ARG A:439 , ALA A:440 , ALA A:441 , ASN A:448 , GLY A:449 , HOH A:961BINDING SITE FOR RESIDUE EDO A 902
02AC2SOFTWARETYR A:242 , LEU A:246 , GLU A:249 , LEU A:428 , LYS A:431 , HIS A:432BINDING SITE FOR RESIDUE EDO A 903
03AC3SOFTWAREPHE A:253 , ASP A:256 , ARG A:257 , HIS A:369 , HOH A:1061BINDING SITE FOR RESIDUE EDO A 904
04AC4SOFTWAREASP A:373 , PHE A:374 , LYS A:375 , HIS A:392 , GLY A:393 , EDO A:909 , HOH A:1093BINDING SITE FOR RESIDUE EDO A 905
05AC5SOFTWAREASP A:313 , MET A:350 , GLY A:412 , ASP A:414 , LYS A:415 , HOH A:991BINDING SITE FOR RESIDUE EDO A 906
06AC6SOFTWAREHIS A:338 , ASP A:394 , LEU A:395 , GLU A:396 , ARG A:426 , POP A:901BINDING SITE FOR RESIDUE EDO A 907
07AC7SOFTWAREARG A:257 , ASP A:365 , HOH A:937 , HOH A:1080BINDING SITE FOR RESIDUE EDO A 908
08AC8SOFTWAREASP A:373 , HIS A:392 , EDO A:905BINDING SITE FOR RESIDUE EDO A 909
09AC9SOFTWARETYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , HOH A:984BINDING SITE FOR RESIDUE EDO A 910
10BC1SOFTWAREGLN A:233 , ALA A:236 , GLU A:237 , HOH A:1075BINDING SITE FOR RESIDUE EDO A 911
11BC2SOFTWAREMET A:300 , ALA A:302 , LEU A:305 , TYR A:306 , ARG A:330 , GLU A:332 , LEU A:339 , PHE A:342 , MET A:344 , ASN A:346 , PHE A:347 , CYS A:348 , TYR A:384 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , TRP A:417 , GLY A:419 , GLY A:421 , GLY A:423 , ARG A:426 , POP A:901 , HOH A:912 , HOH A:1086 , HOH A:1094BINDING SITE FOR RESIDUE YLY A 900
12BC3SOFTWAREARG A:330 , HIS A:338 , GLU A:396 , ARG A:426 , YLY A:900 , EDO A:907 , HOH A:1094BINDING SITE FOR RESIDUE POP A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q7H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:212 -Gly A:213
2Asp A:318 -Pro A:319
3Gly A:385 -Asp A:386
4Gly A:403 -Pro A:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q7H)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q7H)

(-) 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:260
 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 2q7hA01 A:188-239 He    lix hairpin bin             2q7hA02 A:240-454 Bira Bifunctional Prot   ein; Domain 2                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....----...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhh....---.hhhhh.ee...eee...hhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eeeee.......eeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7h A 188 PALTKSQTDRLEVLLNPKDE----SGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGID---ELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 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                                                                279 283
   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 2Q7H)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q7H)

(-) 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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  2q7h
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYLS_METMA | Q8PWY1: 2e3c 2q7e 2q7g 2zce 2zim 2zin 2zio 3qtc 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

2q7e THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO AN ATP ANALOGUE
2q7g THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO A PYRROLYSINE ANALGOUE (CYC) AND ATP
2zim CRYSTAL STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED PYRROLYSINE AND PYROPHOSPHATE, FURTHER REFINED STRUCTURE