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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH ATP
 
Authors :  S. Bilokapic, T. Maier, D. Ahel, I. Gruic-Sovulj, D. Soll, I. Weygand-D N. Ban
Date :  30 Mar 06  (Deposition) - 26 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Zinc Ion, Trna Synthetase, (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  (5, 34)

Asymmetric/Biological Unit (5, 34)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
4MSE26Mod. Amino AcidSELENOMETHIONINE
5ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:304 , CYS A:306 , GLU A:355 , CYS A:461 , ATP A:1505BINDING SITE FOR RESIDUE ZN A1503
2AC2SOFTWARETRP A:245 , TYR A:303 , ALA A:304 , GLN A:305BINDING SITE FOR RESIDUE CL A1504
3AC3SOFTWAREALA B:304 , CYS B:306 , GLU B:355 , CYS B:461BINDING SITE FOR RESIDUE ZN B1503
4AC4SOFTWARETRP B:245 , TYR B:303 , ALA B:304 , GLN B:305BINDING SITE FOR RESIDUE CL B1504
5AC5SOFTWAREARG B:336 , GLU B:338 , ATP B:1507BINDING SITE FOR RESIDUE MG B1505
6AC6SOFTWAREASP B:416 , GLU B:432 , ASN B:435 , ATP B:1507BINDING SITE FOR RESIDUE MG B1506
7AC7SOFTWAREHIS A:250 , TYR A:303 , ALA A:304 , ARG A:336 , GLU A:338 , VAL A:348 , PHE A:351 , ARG A:353 , GLU A:432 , ASN A:435 , GLY A:465 , ARG A:468 , ZN A:1503 , HOH A:2221BINDING SITE FOR RESIDUE ATP A1505
8AC8SOFTWAREARG B:336 , GLU B:338 , ARG B:347 , VAL B:348 , PHE B:351 , ARG B:353 , GLU B:432 , PHE B:433 , ASN B:435 , GLY B:465 , ARG B:468 , MG B:1505 , MG B:1506 , HOH B:2168 , HOH B:2199 , HOH B:2228 , HOH B:2229 , HOH B:2230BINDING SITE FOR RESIDUE ATP B1507

(-) SS Bonds  (0, 0)

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

(-) 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 2CJA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CJA)

(-) 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:477
 aligned with SYS2_METBF | Q46AN5 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:504
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498    
           SYS2_METBF     - --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
                 2cja A  -2 SHmKLQFNLKAYFK--------KDAIAALFEEANSTLLTRGAPEGQGAKVTEWKL---RIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHELRmLKVPYIKSmENIEGGIQLELEVGEAEmKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPmEHPFKEDPTQAmmKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREmIFPKLVTWEVWmKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGmCYAQCPPFWmYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYmHIFNDILDIEWRKARV----------------NTVGTTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSGVGLERWAAVFLAQKGLDPANWPEEFRNRVGEmPKGIRFL 502
                             ||      8   |     -  |     28        38        48    |   58        68        78        88        98       108    |  118   |   128       138 |     148       158       168       178       188||     198       208       218       228     | 238       248       258       268       278       288       298  |    308  |    318       328       338       348       358       368       378       388    |    -         - |     418       428       438       448       458       468       478       488      |498    
                             ||         12       21                              53  57                                                     113-MSE  122-MSE           140-MSE                              177-MSE     189-MSE                                      234-MSE     246-MSE                                                301-MSE   311-MSE                                                           377-MSE         393              410                                                                                  495-MSE   
                            -1|                                                                                                                                                                                          190-MSE                                                                                                                                                                                                                                                                                                                    
                              1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:489
 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.............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
                 2cja B  -3 GSHmKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAKVTEWKLGEDRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHELRmLKVPYIKSmENIEGGIQLELEVGEAEmKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPmEHPFKEDPTQAmmKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREmIFPKLVTWEVWmKSGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGmCYAQCPPFWmYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDRYmHIFNDILDIEWRKARV----------------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|                                                                                                             113-MSE  122-MSE           140-MSE                              177-MSE     189-MSE                                      234-MSE     246-MSE                                                301-MSE   311-MSE                                                           377-MSE         393              410                                                                                  495-MSE   
                               1-MSE                                                                                                                                                                                      190-MSE
   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 2CJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 2cim 2cj9 2cjb

(-) Related Entries Specified in the PDB File

2cim CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE
2cj9 CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH AN ANALOG OF SERYLADENYLATE
2cjb CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH SERINE