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(-) Description

Title :  STRUCTURAL BASIS FOR FULL-SPECTRUM INHIBITION OF THREONYL-TRNA SYNTHETASE BY BORRELIDIN 1
 
Authors :  P. Fang, X. Yu, K. Chen, X. Chen, M. Guo
Date :  09 Mar 14  (Deposition) - 11 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Synthetase, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Fang, X. Yu, S. J. Jeong, A. Mirando, K. Chen, X. Chen, S. Kim, C. S. Francklyn, M. Guo
Structural Basis For Full-Spectrum Inhibition Of Translational Functions On A Trna Synthetase.
Nat Commun V. 6 6402 2015
PubMed-ID: 25824639  |  Reference-DOI: 10.1038/NCOMMS7402

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE, CYTOPLASMIC
    ChainsA, B, C, D
    EC Number6.1.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 322-723
    GeneTARS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTHREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
12CR4Ligand/Ion(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADECA-4,6-DIEN-2-YL]CYCLOPENTANECARBOXYLIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
12CR2Ligand/Ion(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADECA-4,6-DIEN-2-YL]CYCLOPENTANECARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
12CR2Ligand/Ion(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADECA-4,6-DIEN-2-YL]CYCLOPENTANECARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:387 , HIS A:388 , MET A:411 , CYS A:413 , ARG A:442 , GLN A:460 , TYR A:540 , THR A:560 , ASP A:564 , LEU A:567 , HIS A:590binding site for residue 2CR A 800
2AC2SOFTWARECYS A:413 , HIS A:464 , HIS A:590 , HOH A:907binding site for residue ZN A 801
3AC3SOFTWAREGLY B:387 , HIS B:388 , MET B:411 , CYS B:413 , ARG B:442 , TYR B:540 , THR B:560 , ASP B:564 , LEU B:567 , HIS B:590binding site for residue 2CR B 800
4AC4SOFTWARECYS B:413 , HIS B:464 , HIS B:590binding site for residue ZN B 801
5AC5SOFTWAREGLY C:387 , HIS C:388 , MET C:411 , CYS C:413 , ARG C:442 , GLN C:460 , TYR C:540 , THR C:560 , ASP C:564 , LEU C:567 , HIS C:590 , HOH C:906binding site for residue 2CR C 800
6AC6SOFTWARECYS C:413 , HIS C:464 , HIS C:590binding site for residue ZN C 801
7AC7SOFTWAREGLY D:387 , HIS D:388 , MET D:411 , CYS D:413 , ARG D:442 , GLN D:460 , TYR D:540 , THR D:560 , ASP D:564 , LEU D:567 , HIS D:590binding site for residue 2CR D 800
8AC8SOFTWARECYS D:413 , HIS D:464 , HIS D:590binding site for residue ZN D 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P3N)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:430 -Pro A:431
2Leu B:430 -Pro B:431
3Asp B:579 -Gly B:580
4Asp B:692 -Asn B:693
5Leu C:430 -Pro C:431
6Leu D:430 -Pro D:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3N)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3N)

(-) 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:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...............eee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p3n A 322 DHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721  

Chain B from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...hhhhh.......eee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p3n B 322 DHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721  

Chain C from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh..........eeeee..eee...............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...............eeeeeeeeeehhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p3n C 322 DHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721  

Chain D from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh...ee.....eeeee..eee...............eee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...ee..........eeeeee...hhhhhhhhhhhhhh...hhhhh...eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p3n D 322 DHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721  

   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 4P3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3N)

(-) Gene Ontology  (17, 17)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYTC_HUMAN | P266391wwt 4hwt 4ttv

(-) Related Entries Specified in the PDB File

4p3o 4p3p