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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH METHIONINE
 
Authors :  H. Ingvarsson, T. A. Jones, T. Unge
Date :  31 Dec 09  (Deposition) - 28 Jul 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide-Binding, Protein Biosynthesis, Ligase, Aminoacyl-Trna Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ingvarsson, T. Unge
Flexibility And Communication Within The Structure Of The Mycobacterium Smegmatis Methionyl-Trna Synthetase.
Febs J. V. 277 3947 2010
PubMed-ID: 20796028  |  Reference-DOI: 10.1111/J.1742-4658.2010.07784.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE
    Atcc: 700084
    Chains: A
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET 101 D-TOPO
    Fragment: RESIDUES 2-515
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: MC2 155

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
12HP1Ligand/IonDIHYDROGENPHOSPHATE ION
2CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
3MET1Mod. Amino AcidMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:11 , ALA A:12 , TYR A:13 , ASP A:50 , TRP A:230 , ALA A:233 , TYR A:237 , ILE A:266 , HIS A:270BINDING SITE FOR RESIDUE MET A 600
2AC2SOFTWAREPRO A:188 , ASP A:189 , ARG A:288 , VAL A:406BINDING SITE FOR RESIDUE 2HP A 601
3AC3SOFTWAREALA A:114 , GLY A:115 , ASP A:116 , ARG A:167 , ALA A:170 , TYR A:171 , ARG A:174 , TYR A:452 , ARG A:495BINDING SITE FOR RESIDUE CXS A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X1M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:187 -Pro A:188
2Phe A:243 -Pro A:244
3Trp A:255 -Pro A:256
4Val A:406 -Pro A:407

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X1M)

(-) Exons   (0, 0)

(no "Exon" information available for 2X1M)

(-) 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:512
 aligned with A0R3E2_MYCS2 | A0R3E2 from UniProtKB/TrEMBL  Length:515

    Alignment length:513
                                    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       511   
         A0R3E2_MYCS2     2 SEPFYITTAIAYPNGVPHIGHAYEYIATDAIARFKRLDGYDVRYLTGTDVHGQKMAETAAKEGIPAAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKAIWKRMADAGDIYLDAYKGWYSIRDERFFTENETTEQPDGTRIATETGAPVTWTEEQTYFFRLSAYTDRLLALYEEHPEFIGPDARRNEIVSFVSGGLKDLSISRTTFDWGVPVPDHPDHVMYVWVDALTNYLTGVGFPDTESESFRRYWPADLHMIGKDIIRFHTVYWPAFLMSAGLPLPKRIFAHGWLLNRGEKMSKSIGNVVDPVNLVDTFGLDQVRYFLLREVPFGQDGSYNEDAIIGRVNADLANELGNLAQRSLSMVAKNLGAAVPDPGEFTDEDTALLAAADALLERVREHFDVPAMHLALEAIWSVLGAANRYFSAQEPWVLRKSDAAEDQQRFRTVLYTTLEVVRIASLLLQPVMPESTAKLLDLLGQPTDERDFSAIANRIKPGTSLPAPSGIFPRYQN 514
               SCOP domains d2x1ma1 A:2-135,A:136-353 automated matches                                                                                           d2x1ma1 A:2-135,A:136-353 automated matches                                                                                                                                                                               d2x1ma2 A:354-512 automated matches                                                                                                                            -- SCOP domains
               CATH domains 2x1mA01 A:2-115,A:230-340 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                   2x1mA02 A:116-229  [code=2.170.220.10, no name defined]                                                           2x1mA01 A:2-115,A:230-340 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---tRNA-synt_1g-2x1mA01 A:5-365                                                                                                                                                                                                                                                                                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee....eee.....eee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......hhhhh....................-. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x1m A   2 SEPFYITTAIAYPNGVPHIGHAYEYIATDAIARFKRLDGYDVRYLTGTDVHGQKMAETAAKEGIPAAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKAIWKRMADAGDIYLDAYKGWYSIRDERFFTENETTEQPDGTRIATETGAPVTWTEEQTYFFRLSAYTDRLLALYEEHPEFIGPDARRNEIVSFVSGGLKDLSISRTTFDWGVPVPDHPDHVMYVWVDALTNYLTGVGFPDTESESFRRYWPADLHMIGKDIIRFHTVYWPAFLMSAGLPLPKRIFAHGWLLNRGEKMSKSIGNVVDPVNLVDTFGLDQVRYFLLREVPFGQDGSYNEDAIIGRVNADLANELGNLAQRSLSMVAKNLGAAVPDPGEFTDEDTALLAAADALLERVREHFDVPAMHLALEAIWSVLGAANRYFSAQEPWVLRKSDAAEDQQRFRTVLYTTLEVVRIASLLLQPVMPESTAKLLDLLGQPTDERDFSAIANRIKPGTSLPAPSGIFPRY-M 600
                                    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       511| |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        512 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          600
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A0R3E2_MYCS2 | A0R3E2)
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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(-) Related Entries Specified in the PDB File

2x1l CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH METHIONINE AND ADENOSINE