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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONYL-TRNA SYNTHETASE METRS FROM BRUCELLA MELITENSIS BOUND TO SELENOMETHIONINE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  06 Feb 12  (Deposition) - 15 Feb 12  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Class Ia Aminoacyl-Trna Synthetase, Selenomethionine, Anomalous Signal, Protein Synthesis, Atp- Dependent, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Ojo, R. M. Ranade, Z. Zhang, D. M. Dranow, J. B. Myers, R. Choi, S. Nakazawa Hewitt, T. E. Edwards, D. R. Davies, D. Lorimer, S. M. Boyle, L. K. Barrett, F. S. Buckner, E. Fan, W. C. Van Voorhis
Brucella Melitensis Methionyl-Trna-Synthetase (Metrs), A Potential Drug Target For Brucellosis.
Plos One V. 11 60350 2016
PubMed-ID: 27500735  |  Reference-DOI: 10.1371/JOURNAL.PONE.0160350

(-) Compounds

Molecule 1
    Chains: A, B, C
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: BAB1_1014, METG
    Organism Scientific: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308
    Organism Taxid: 359391
    Synthetase, Class Ia: METHIONYL-TRNA SYNTHETASE, CLASS IA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. ResidueSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. ResidueSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. ResidueSELENOMETHIONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. ResidueSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4DLP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Met A:187 -Pro A:188
2Tyr A:243 -Pro A:244
3Trp A:254 -Pro A:255
4Met B:187 -Pro B:188
5Tyr B:243 -Pro B:244
6Trp B:254 -Pro B:255
7Met C:187 -Pro C:188
8Tyr C:243 -Pro C:244
9Trp C:254 -Pro C:255

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DLP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DLP)

(-) 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:493
 aligned with Q2YQ76_BRUA2 | Q2YQ76 from UniProtKB/TrEMBL  Length:515

    Alignment length:507
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       
         Q2YQ76_BRUA2     3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRGEKMSKSVGNVIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRYV 509
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhhhhee.....ee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.--............eehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..ee.------------.hhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dlp A   3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRT--DWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFN------------IDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRYV 509
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        |- |     222       232       242       252       262       272       282       292   |     -      |312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       
                                                                                                                                                                                                                                          211  |                                                                               296          309                                                                                                                                                                                                        
                                                                                                                                                                                                                                             214                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:464
 aligned with Q2YQ76_BRUA2 | Q2YQ76 from UniProtKB/TrEMBL  Length:515

    Alignment length:507
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       
         Q2YQ76_BRUA2     2 SREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRGEKMSKSVGNVIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeee.-------------------------------.eeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee...............eehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..ee.------------.hhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dlp B   2 SREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGW-------------------------------WVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFN------------IDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
                                    11        21        31        41        51        61        71        81        91       101       111       121    |    -         -         -      |161       171       181       191       201       211       221       231       241       251       261       271       281       291    |    -       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       
                                                                                                                                                      126                             158                                                                                                                                       296          309                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:468
 aligned with Q2YQ76_BRUA2 | Q2YQ76 from UniProtKB/TrEMBL  Length:515

    Alignment length:506
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502      
         Q2YQ76_BRUA2     3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRGEKMSKSVGNVIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeee....---------------------------..eeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee...............eehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..eee.-----------.hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dlp C   3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSV---------------------------EWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNR-----------IDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
                                    12        22        32        42        52        62        72        82        92       102       112       122      |  -         -         -    |  162       172       182       192       202       212       222       232       242       252       262       272       282       292    |    -      |312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502      
                                                                                                                                                        129                         157                                                                                                                                         297         309
   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 4DLP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q2YQ76_BRUA2 | Q2YQ76)
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:0004825    methionine-tRNA ligase activity    Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
    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.
biological process
    GO:0006431    methionyl-tRNA aminoacylation    The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-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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  6.1.1.10
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 Related Entries

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

UniProtKB/TrEMBL
        Q2YQ76_BRUA2 | Q2YQ76: 4py2

(-) Related Entries Specified in the PDB File

3sp1 CYSRS FROM B. BURGDORFERI
3tze TRPRS FROM E. CUNICULI RELATED ID: BRABA.10201.A RELATED DB: TARGETTRACK