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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE
 
Authors :  S. Bilokapic, T. Maier, D. Ahel, I. Gruic-Sovulj, D. Soll, I. Weygand-D N. Ban
Date :  24 Mar 06  (Deposition) - 26 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Trna Synthetase, Zinc Ion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bilokapic, T. Maier, D. Ahel, I. Gruic-Sovulj, D. Soll, I. Weygand-Durasevic, N. Ban
Structure Of The Unusual Seryl-Trna Synthetase Reveals A Distinct Zinc-Dependent Mode Of Substrate Recognition
Embo J. V. 25 2498 2006
PubMed-ID: 16675947  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601129

(-) Compounds

Molecule 1 - SERYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 269797
    Other Details: ZINC ION IN ACTIVE SITE
    Strain: FUSARO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PT1Ligand/IonPLATINUM (II) ION
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:306 , GLU A:355 , CYS A:461 , HOH A:2070BINDING SITE FOR RESIDUE ZN A1503
2AC2SOFTWARETRP A:245 , TYR A:303 , ALA A:304 , GLN A:305BINDING SITE FOR RESIDUE CL A1504
3AC3SOFTWARECYS B:306 , GLU B:355 , CYS B:461BINDING SITE FOR RESIDUE ZN B1503
4AC4SOFTWARETRP B:245 , TYR B:303 , ALA B:304 , GLN B:305 , PRO B:307BINDING SITE FOR RESIDUE CL B1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:323 -Pro A:324
2Ile B:323 -Pro B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CIM)

(-) 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:487
 aligned with SYS2_METBF | Q46AN5 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:502
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500  
           SYS2_METBF     1 MKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAKVTEWKLGEDRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPMEHPFKEDPTQAMMKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGMCYAQCPPFWMYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYMHIFNDILDIEWRKARVTPWFMAQEGLLGLAEENTVGTTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSGVGLERWAAVFLAQKGLDPANWPEEFRNRVGEMPKGIRFL 502
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.........hhhhhhhhhhhhh.............eeeeeee....eeeeeee.....hhhhhhhhhhhhhhhh..........eeeeeeeeeee............eeeeee..eeeeeee...hhhhhh.hhhhhhhhhhhhhhhhh........eeeee...........hhhhhhhh..eee......eee.hhhhhhhhhhhhhhhhh.hhhh..eeee...eeehhhhhhh...........eee......hhhhhhhhhhhhhh....hhhhhhh.....eee....hhhhhhhh.eeee......eeeee...eee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.---------------...eeeeeee...........eeeeeeee..hhhhhh.eeeee.....eeeeeeeehhhhhhhhhhhh........hhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cim A   1 MKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAKVTEWKLGEDRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPMEHPFKEDPTQAMMKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGMCYAQCPPFWMYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYMHIFNDILDIEWRKARVT---------------NTVGTTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSGVGLERWAAVFLAQKGLDPANWPEEFRNRVGEMPKGIRFL 502
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   |     -       410       420       430       440       450       460       470       480       490       500  
                                                                                                                                                                                                                                                                                                                                                                                                                                   394             410                                                                                            


Chain B from PDB  Type:PROTEIN  Length:477
 aligned with SYS2_METBF | Q46AN5 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:505
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       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       457       467       477       487       497     
           SYS2_METBF     - ---MKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAKVTEWKLGEDRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPMEHPFKEDPTQAMMKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGMCYAQCPPFWMYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYMHIFNDILDIEWRKARVTPWFMAQEGLLGLAEENTVGTTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSGVGLERWAAVFLAQKGLDPANWPEEFRNRVGEMPKGIRFL 502
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.........hhhhhhhhhhhhh.............eeeeee---..eeeeeee.....hhhhhhhhhhhhhhhh....------eeeeeeeeeee............eeeeee..eeeeeee...hhhhhh.hhhhhhhhhhhhhhhhh.----...eeeee...........hhhhhhhh..eee......eee.hhhhhhhhhhhhhhhhh.hhhh..eeee...eeehhhhhhh...........eee......hhhhhhhhhhhhhh....hhhhhhh.....eee....hhhhhhhh.eeee......eeeee...eee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.---------------...eeeeeee...........eeeeeeee..hhhhhh.eeeee.....eeeeeeeehhhhhhhhhhhh........hhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cim B  -3 GSHMKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAKVTEWK---DRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKY------IEVESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKNRVPDRILTLLEEKIEAAQY----EHWNLLWQREPMEHPFKEDPTQAMMKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGMCYAQCPPFWMYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYMHIFNDILDIEWRKARVT---------------NTVGTTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSGVGLERWAAVFLAQKGLDPANWPEEFRNRVGEMPKGIRFL 502
                              ||     7        17        27        37        47    |   57        67        77        87 |      97       107       117       127       137       147       157   |   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      |  -         -  |    417       427       437       447       457       467       477       487       497     
                             -1|                                                 52  56                               89     96                                                              161  166                                                                                                                                                                                                                                 394             410                                                                                            
                               1
   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 2CIM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CIM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYS2_METBF | Q46AN5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004828    serine-tRNA ligase activity    Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016260    selenocysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteine, an essential component of glutathione peroxidase and some other proteins.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.
    GO:0006434    seryl-tRNA aminoacylation    The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    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
        SYS2_METBF | Q46AN5: 2cj9 2cja 2cjb

(-) Related Entries Specified in the PDB File

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