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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE (MST1) IN COMPLEX WITH THE CANONICAL TRNATHR AND THREONYL SULFAMOYL ADENYLATE
 
Authors :  K. M. Holman, M. Simonovic
Date :  23 Mar 15  (Deposition) - 06 Jan 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aminoacyl-Trna Synthetase, Thrrs, Mst1, Trna, Ribonucleoprotein Complex, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Holman, J. Wu, J. Ling, M. Simonovic
The Crystal Structure Of Yeast Mitochondrial Thrrs In Complex With The Canonical Threonine Trna.
Nucleic Acids Res. V. 44 1428 2016
PubMed-ID: 26704982  |  Reference-DOI: 10.1093/NAR/GKV1501

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MST1, YKL194C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: THREONYL-TRNA SYNTHETASE,THRRS
 
Molecule 2 - TRNA
    Chains: C, D
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2TSB2Ligand/Ion5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:133 , HIS A:184 , HIS A:319 , TSB A:502binding site for residue ZN A 501
2AC2SOFTWAREMET A:131 , CYS A:133 , ARG A:162 , GLU A:164 , THR A:173 , ARG A:174 , LEU A:175 , PHE A:178 , GLN A:180 , ASP A:182 , HIS A:184 , TYR A:270 , GLN A:287 , VAL A:288 , THR A:290 , GLN A:292 , HIS A:319 , GLY A:324 , SER A:325 , ARG A:328 , ZN A:501binding site for residue TSB A 502
3AC3SOFTWARETRP A:390 , LYS A:459 , HOH A:689binding site for residue SO4 A 503
4AC4SOFTWARETHR A:188 , PRO A:189 , SER A:190 , HOH A:601 , HOH A:609binding site for residue SO4 A 504
5AC5SOFTWAREPHE A:225 , ASN A:227 , LYS A:261 , MET A:277 , THR A:285binding site for residue SO4 A 505
6AC6SOFTWARECYS B:133 , HIS B:184 , HIS B:319 , TSB B:502binding site for residue ZN B 501
7AC7SOFTWAREMET B:131 , CYS B:133 , ARG B:162 , GLU B:164 , THR B:173 , ARG B:174 , LEU B:175 , PHE B:178 , GLN B:180 , ASP B:182 , HIS B:184 , TYR B:270 , GLN B:287 , VAL B:288 , GLN B:292 , HIS B:319 , GLY B:324 , SER B:325 , ARG B:328 , ZN B:501 , HOH B:703binding site for residue TSB B 502
8AC8SOFTWAREILE B:236 , GLY B:237 , ARG B:300 , HOH B:606binding site for residue SO4 B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:150 -Pro A:151
2Leu B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YYE)

(-) 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:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh.....eee........eee...hhhhhhhhhhh..ee.hhh.eeeee..eee...hhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeeeeeeehhhhhhhhhhhhh...hhhhh...eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.......eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yye A  36 ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTDEEKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      |224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454        
                                                                                                                                                                                                          212|                                                                                                                                                                                                                                                
                                                                                                                                                                                                           222                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh.....eee........eee...hhhhhhhhhhhh..hhhhh.eeeee..eee...hhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...ee.....ee..eeeeeeeeeehhhhhhhhhhhhh...hhhhh...eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yye B  36 ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTDEEKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNKSFEKLTMSQIWEKFIELEKNYK 462
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      |224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   ||  445       455       
                                                                                                                                                                                                          212|                                                                                                                                                                                                                     438|                      
                                                                                                                                                                                                           222                                                                                                                                                                                                                      440                      


Chain C from PDB  Type:RNA  Length:74
                                                                                                          
                 4yye C   1 GUUAUAUUAGCUUAAUUGGUAGAGCAUUCGUUUUGUAAUCGAAAGGUUUGGGGUUCAAAUCCCUAAUAUAACAC  74
                                    10        20        30        40        50        60        70    


Chain D from PDB  Type:RNA  Length:74
                                                                                                          
                 4yye D   1 GUUAUAUUAGCUUAAUUGGUAGAGCAUUCGUUUUGUAAUCGAAAGGUUUGGGGUUCAAAUCCCUAAUAUAACAC  74
                                    10        20        30        40        50        60        70
   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 4YYE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        SYTM_YEAST | P07236: 3ugq 3ugt 3uh0 4eo4

(-) Related Entries Specified in the PDB File

3ugq 3ugt 3uh0 4eo4