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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF TRYPTOPHANYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH INDOLMYCIN AND MG*ATP
 
Authors :  T. Williams, W. Y. Yin, C. W. Carter Jr.
Date :  02 Sep 15  (Deposition) - 18 Nov 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Aars, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. L. Williams, Y. W. Yin, C. W. Carter
Selective Inhibition Of Bacterial Tryptophanyl-Trna Synthetases By Indolmycin Is Mechanism-Based.
J. Biol. Chem. V. 291 255 2016
PubMed-ID: 26555258  |  Reference-DOI: 10.1074/JBC.M115.690321

(-) Compounds

Molecule 1 - TRYPTOPHAN--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRPS
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: TRYPTOPHANYL-TRNA SYNTHETASE,TRPRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
15BX1Ligand/Ion(5S)-5-[(1R)-1-(1H-INDOL-3-YL)ETHYL]-2-(METHYLAMINO)-1,3-OXAZOL-4(5H)-ONE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
5MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
15BX2Ligand/Ion(5S)-5-[(1R)-1-(1H-INDOL-3-YL)ETHYL]-2-(METHYLAMINO)-1,3-OXAZOL-4(5H)-ONE
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:8 , GLN A:9 , SER A:11 , GLY A:17 , ASN A:18 , GLY A:21 , LYS A:111 , VAL A:143 , GLY A:144 , ASP A:146 , GLY A:180 , ALA A:181 , ARG A:182 , ILE A:183 , LYS A:192 , MSE A:193 , SER A:194 , LYS A:195 , SER A:196 , MG A:402 , 5BX A:404 , HOH A:520 , HOH A:525 , HOH A:537 , HOH A:548 , HOH A:589 , HOH A:591 , HOH A:619binding site for residue ATP A 401
2AC2SOFTWAREGLN A:9 , ATP A:401 , 5BX A:404 , HOH A:525 , HOH A:589 , HOH A:591binding site for residue MG A 402
3AC3SOFTWARELYS A:218 , THR A:222 , TYR A:265 , GLY A:266 , LYS A:269binding site for residue GOL A 403
4AC4SOFTWAREPHE A:5 , SER A:6 , GLY A:7 , GLN A:9 , HIS A:43 , TYR A:125 , MSE A:129 , ASP A:132 , VAL A:143 , GLN A:147 , ATP A:401 , MG A:402 , HOH A:525 , HOH A:589binding site for residue 5BX A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DK4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DK4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DK4)

(-) Exons   (0, 0)

(no "Exon" information available for 5DK4)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dk4 A   0 GmKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWmLQCIVYIGELERmTQFKEKSAGKEAVSAGLLTYPPLmAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARImSLVDPTKKmSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWmESEELDRVLDEGAEKANRVASEmVRKmEQAmGLGRR 327
                             |       9        19        29        39        49        59        69        79        89  |     99     | 109       119       129       139       149       159       169       179    |  189   |   199       209       219       229       239       249       259       269       279       289 |     299       309    |  319  |     
                             |                                                                                         92-MSE      105-MSE                 129-MSE                                                184-MSE  193-MSE                                                                                           291-MSE                314-MSE   |     
                             1-MSE                                                                                                                                                                                                                                                                                                                      318-MSE     
                                                                                                                                                                                                                                                                                                                                                            322-MSE
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  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 5DK4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DK4)

(-) Gene Ontology  (9, 9)

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 Related Entries

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UniProtKB/Swiss-Prot
        SYW_GEOSE | P00953: 1d2r 1i6k 1i6l 1i6m 1m83 1mau 1maw 1mb2 2ov4 3fhj 3fi0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DK4)