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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE (MST1) IN COMPLEX WITH SERYL SULFAMOYL ADENYLATE
 
Authors :  K. M. Peterson, J. Ling, I. Simonovic, D. Soll, M. Simonovic
Date :  13 Apr 12  (Deposition) - 11 Jul 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Aminoacyl-Trna Synthetase Class Ii, Threonyl-Trna Synthetase, Threonine Trna, Mitochondria, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ling, K. M. Peterson, I. Simonovic, D. Soll, M. Simonovic
The Mechanism Of Pre-Transfer Editing In Yeast Mitochondria Threonyl-Trna Synthetase.
J. Biol. Chem. V. 287 28518 2012
PubMed-ID: 22773845  |  Reference-DOI: 10.1074/JBC.M112.372920

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE, MITOCHONDRIAL
    Chains: A, B, C, D
    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
    Fragment: UNP RESIDUES 26-462
    Gene: MST1, YKL194C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: THREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1SSA8Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SSA4Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SSA4Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:131 , ARG A:162 , GLU A:164 , THR A:173 , ARG A:174 , LEU A:175 , PHE A:178 , GLN A:180 , ASP A:182 , GLN A:287 , VAL A:288 , GLN A:292 , HIS A:319 , GLY A:324 , SER A:325 , ARG A:328 , ZN A:1003 , HOH A:1101BINDING SITE FOR RESIDUE SSA A 1001
02AC2SOFTWAREVAL A:403 , GLY A:404 , ILE A:407 , LYS A:408 , ILE A:411 , ARG A:434 , ARG A:439 , HOH A:1217 , HOH A:1218 , HOH A:1219 , HOH A:1220BINDING SITE FOR RESIDUE SSA A 1002
03AC3SOFTWARECYS A:133 , HIS A:184 , HIS A:319 , SSA A:1001BINDING SITE FOR RESIDUE ZN A 1003
04AC4SOFTWAREMET 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 , GLN B:287 , VAL B:288 , GLN B:292 , HIS B:319 , GLY B:324 , SER B:325 , ARG B:328 , ZN B:1003 , HOH B:1107BINDING SITE FOR RESIDUE SSA B 1001
05AC5SOFTWAREVAL B:403 , GLY B:404 , LYS B:408 , ILE B:411 , ARG B:434 , ARG B:436 , ARG B:439 , HOH B:1192 , HOH B:1193 , HOH B:1194 , HOH B:1195BINDING SITE FOR RESIDUE SSA B 1002
06AC6SOFTWARECYS B:133 , HIS B:184 , HIS B:319 , SSA B:1001BINDING SITE FOR RESIDUE ZN B 1003
07AC7SOFTWAREMET C:131 , ARG C:162 , GLU C:164 , THR C:173 , ARG C:174 , LEU C:175 , PHE C:178 , GLN C:180 , ASP C:182 , TYR C:270 , LYS C:273 , GLN C:287 , VAL C:288 , GLN C:292 , HIS C:319 , GLY C:324 , SER C:325 , ARG C:328 , ZN C:1003 , HOH C:1135 , HOH C:1137BINDING SITE FOR RESIDUE SSA C 1001
08AC8SOFTWARELYS B:408 , HOH B:1195 , VAL C:403 , LYS C:408 , ILE C:411 , ARG C:434 , ARG C:439 , HOH C:1157 , HOH C:1165 , HOH C:1166BINDING SITE FOR RESIDUE SSA C 1002
09AC9SOFTWARECYS C:133 , HIS C:184 , HIS C:319 , SSA C:1001BINDING SITE FOR RESIDUE ZN C 1003
10BC1SOFTWAREMET D:131 , CYS D:133 , ARG D:162 , GLU D:164 , THR D:173 , LEU D:175 , PHE D:178 , GLN D:180 , ASP D:182 , TYR D:270 , LYS D:273 , GLN D:287 , VAL D:288 , GLN D:292 , GLY D:324 , SER D:325 , ARG D:328 , ZN D:1003 , HOH D:1129BINDING SITE FOR RESIDUE SSA D 1001
11BC2SOFTWAREHOH A:1220 , VAL D:403 , LYS D:408 , ARG D:434 , ARG D:439 , HOH D:1156 , HOH D:1157BINDING SITE FOR RESIDUE SSA D 1002
12BC3SOFTWARECYS D:133 , HIS D:184 , HIS D:319 , SSA D:1001BINDING SITE FOR RESIDUE ZN D 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EO4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:150 -Pro A:151
2Leu B:150 -Pro B:151
3Leu C:150 -Pro C:151
4Leu D:150 -Pro D:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EO4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EO4)

(-) 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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh....eeee....eee...hhhhhhhhhh..........eeeee..eee...............eee..eeeeee...hhhhhhhhhhhhhhhhhhh.........eeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...ee.....ee..eeeeee...hhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee..eeeeeeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eo4 A  36 ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPFAESNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    45        55        65        75        85        95       105       115  ||   129       139       149       159       169       179       189       199       209   ||  225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
                                                                                                            118|                                                                                       213|                                                                                                                                                                                                                                                  
                                                                                                             123                                                                                        220                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhh....hhhhh.eee....eee...hhhhhhhhhh...ee.....eeeee..eee...............eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh.......eeeee........hhhhhhhhhhhhhhhhhhhh..eee..........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeeeeeeehhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.......eeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eo4 B  38 MTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPFSNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    47        57        67        77        87        97       107       117||     131       141       151       161       171       181       191       201       211 ||    229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459   
                                                                                                          118|                                                                                       213|                                                                                                                                                                                                                                                
                                                                                                           123                                                                                        222                                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh....eeee......eee...hhhhhhhhhh....hhhhh.eeeee..eee...............eee..eeeeee...hhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeee...hhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh..................eee.......hhhhhhhhh....eeeeehhhhhhhh.eeeee.......eeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eo4 C  36 ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTEKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    45        55        65        75        85        95       105       115   ||  127       137       147       157       167       177       187       197       207    || 226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456      
                                                                                                             119|                                                                                       212|                                                                                                                                                                                                                                                
                                                                                                              122                                                                                        222                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.ee.........eehhhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhh..........eeee....eee...hhhhhhhhhh..........eeeee..eee...............eee..eeeeee...hhhhhhhhhhhhhhhhh........eeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeee...hhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh..................eee.....hhhhhhhhhhhh...eeeeehhhhhhhh.eeeee.......eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eo4 D  36 ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFGFNEVVTPLIYKKTLWEKSGHWENYADDMFKVETKEEYGLKPMNCPGHCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTPSQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNHAEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMSQIWEKFIELEKNYK 462
                                    45        55        65        75        85        95       105       115  ||   129       139       149       159       169       179       189       199       209  ||   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458    
                                                                                                            118|                                                                                      212|                                                                                                                                                                                                                                                
                                                                                                             123                                                                                       222
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  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 4EO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EO4)

(-) Gene Ontology  (13, 13)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3ugq CRYSTAL STRUCTURE OF THE APO FORM OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE DETERMINED AT 2.1 ANGSTROM RESOLUTION
3ugt CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE - ORTHORHOMBIC CRYSTAL FORM
3uh0 CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE (MST1) IN COMPLEX WITH THREONYL SULFAMOYL ADENYLATE