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(-) Description

Title :  CRYSTAL STRUCTURE OF T. CRUZI HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH 3-METHOXYPYRIDINE (CHEM 443)
 
Authors :  C. -Y. Koh, W. G. J. Hol
Date :  15 Mar 15  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Aars, Hisrs, Trypanosoma Cruzi, Protein-Inhibitor Complex, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -Y. Koh, L. Kallur Siddaramaiah, R. M. Ranade, J. Nguyen, T. Jian, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. M. J. Verlinde, E. Fan, W. G. J. Hol
A Binding Hotspot In The Trypanosoma Cruzi Histidyl-Trna Synthetase Revealed By Fragment-Based Crystallographic Cocktail Screens
Acta Crystallogr. , Sect. D V. 71 1684 2015
PubMed: search  |  Reference-DOI: 10.1107/S1399004715007683

(-) Compounds

Molecule 1 - HISTIDYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 45-478
    Gene: TC00.1047053507019.40
    Organism Scientific: TRYPANOSOMA CRUZI (STRAIN CL BRENER)
    Organism Taxid: 353153
    Strain: CL BRENER

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
12822Ligand/Ion3-METHOXYPYRIDINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4HIS2Mod. Amino AcidHISTIDINE
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
12821Ligand/Ion3-METHOXYPYRIDINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4HIS1Mod. Amino AcidHISTIDINE
5SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:126 , THR A:128 , GLN A:170 , ASN A:172 , ASP A:174 , LEU A:316 , TYR A:318 , TYR A:319 , TYR A:342 , GLY A:359 , PHE A:360 , GLY A:361 , HOH A:613 , HOH A:614 , HOH A:637 , HOH A:667binding site for residue HIS A 501
02AC2SOFTWAREPRO A:125 , CYS A:154 , TRP A:155 , ARG A:156 , ARG A:165 , ARG A:166 , GLU A:167 , HIS A:168 , HOH A:640binding site for residue 282 A 502
03AC3SOFTWAREARG A:69 , HOH A:601 , HOH A:669 , ARG B:69 , HIS B:76binding site for residue SO4 A 503
04AC4SOFTWAREARG A:165 , HIS A:168 , ARG A:334 , GLY A:363 , ASP A:364 , CYS A:365 , VAL A:366 , HOH A:640binding site for residue SO4 A 504
05AC5SOFTWARETHR A:115 , HIS A:119 , TYR B:157 , ARG B:166binding site for residue EDO A 505
06AC6SOFTWAREARG A:196 , SER A:202 , TRP A:305binding site for residue GOL A 506
07AC7SOFTWAREGLU B:126 , THR B:128 , GLN B:170 , ASN B:172 , ASP B:174 , LEU B:316 , TYR B:318 , TYR B:319 , TYR B:342 , GLY B:359 , PHE B:360 , GLY B:361 , HOH B:618 , HOH B:633 , HOH B:680 , HOH B:685binding site for residue HIS B 501
08AC8SOFTWAREPRO B:125 , CYS B:154 , TRP B:155 , ARG B:156 , ARG B:166 , GLU B:167 , HIS B:168 , HOH B:603binding site for residue 282 B 502
09AC9SOFTWAREARG B:165 , HIS B:168 , GLY B:363 , ASP B:364 , CYS B:365 , VAL B:366 , HOH B:603binding site for residue SO4 B 503
10AD1SOFTWARETYR A:157 , ARG A:166 , THR B:115 , GLY B:117binding site for residue EDO B 504
11AD2SOFTWAREARG A:404 , ARG B:196 , SER B:202 , TYR B:302 , TRP B:305binding site for residue GOL B 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:144 -Pro A:145
2Leu B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YRM)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh....hhhhhh..eee.....eeee...hhhhhhhhhhhhhhhh...eeeee..eee......eeeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrm A  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMIPREEVEAQLAVLGLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157||     172       182       192       202       212       222       232      |244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454 ||    476 ||
                                                                                                                                        158|                                                                        239|                                                                                                                                                                                                                   456|      478|
                                                                                                                                         164                                                                         242                                                                                                                                                                                                                    469       501


Chain B from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh....hhhhhh..eee.....eeee...hhhhhhhhhhhhhhhh...eeeee..eee......eeeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrm B  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMEKIPREEVEAQLAVLGLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157||     172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   ||  474   ||
                                                                                                                                        158|                                                                                                                                                                                                                                                                                                 456|      478|
                                                                                                                                         164                                                                                                                                                                                                                                                                                                  469       501
   Legend:   → Mismatch (orange background)
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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 4YRM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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  4yrm
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 Related Entries

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UniProtKB/TrEMBL
        Q4DA54_TRYCC | Q4DA54: 3hrk 3lc0 4yp0 4ypf 4yrc 4yre 4yrf 4yrg 4yri 4yrj 4yrk 4yrl 4yrn 4yro 4yrp 4yrq 4yrr 4yrs 4yrt

(-) Related Entries Specified in the PDB File

4yp0 4ypf 4yrc 4yre 4yrf 4yrg 4yri 4yrj 4yrk 4yrl 4yrn 4yro 4yrp 4yrq 4yrr 4yrs 4yrt