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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH COMPOUND CHEM 89
 
Authors :  C. Y. Koh, J. E. Kim, S. Shibata, E. Fan, C. L. M. J. Verlinde, W. G. J. Hol
Date :  30 Mar 12  (Deposition) - 12 Sep 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminoacyl-Trna Synthetase, Aars, Metrs, Parasite, Ligase, Protein- Inhibitor Complex, Rossmann-Fold, Translation, Nucleotide Binding, , Rossmann Fold, Trna Binding, Atp Binding, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Koh, J. E. Kim, S. Shibata, R. M. Ranade, M. Yu, J. Liu, J. R. Gillespie, F. S. Buckner, C. L. Verlinde, E. Fan, W. G. Hol
Distinct States Of Methionyl-Trna Synthetase Indicate Inhibitor Binding By Conformational Selection.
Structure V. 20 1681 2012
PubMed-ID: 22902861  |  Reference-DOI: 10.1016/J.STR.2012.07.011

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE, PUTATIVE
    Chains: A, B
    EC Number: 6.1.1.10
    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: RESIDUES 237-773
    Gene: TB10.70.6470
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 999953
    Strain: 927/4 GUTAT10.1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
10P61Ligand/Ion2-AMINOQUINOLIN-8-OL
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL20Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
10P6-1Ligand/Ion2-AMINOQUINOLIN-8-OL
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL10Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 2 (4, 13)
No.NameCountTypeFull Name
10P61Ligand/Ion2-AMINOQUINOLIN-8-OL
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL10Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:345 , GLU A:349 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREARG A:271 , SER A:714 , PRO A:718 , SER A:721 , VAL A:722 , HOH A:953 , HOH A:1031 , HOH A:1032BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWARELYS A:382 , HIS A:395 , VAL A:396 , HOH A:1021BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREARG A:719BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREHIS A:289 , LYS A:338 , TRP A:459 , ALA A:460BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWARELYS A:276 , PHE A:741 , HOH A:982BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWAREGLY A:573 , TYR A:574 , ASP A:575 , ALA A:576 , LYS A:720BINDING SITE FOR RESIDUE GOL A 808
09AC9SOFTWAREPRO A:731 , GLU A:732 , VAL A:733 , HOH A:1103BINDING SITE FOR RESIDUE GOL A 809
10BC1SOFTWARELEU A:520 , DMS A:811 , DMS A:812BINDING SITE FOR RESIDUE DMS A 810
11BC2SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , ILE A:519 , LEU A:520 , LYS A:521 , DMS A:810BINDING SITE FOR RESIDUE DMS A 811
12BC3SOFTWARELEU A:444 , DMS A:810 , DMS A:813 , HOH A:1083BINDING SITE FOR RESIDUE DMS A 812
13BC4SOFTWAREPHE A:370 , LYS A:521 , TYR A:526 , DMS A:812BINDING SITE FOR RESIDUE DMS A 813
14BC5SOFTWARELYS A:686 , THR A:690 , ARG B:434 , ARG B:438BINDING SITE FOR RESIDUE GOL A 814
15BC6SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , ILE A:519 , HIS A:523 , HOH A:1013BINDING SITE FOR RESIDUE MET A 815
16BC7SOFTWARETYR B:324 , SER B:325 , ILE B:326BINDING SITE FOR RESIDUE DMS B 801
17BC8SOFTWARELYS B:347 , LEU B:482 , ARG B:486BINDING SITE FOR RESIDUE GOL B 802
18BC9SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 803
19CC1SOFTWAREARG B:271 , ARG B:274 , SER B:714 , PRO B:718 , HOH B:991BINDING SITE FOR RESIDUE GOL B 804
20CC2SOFTWARETYR A:305 , HIS B:289 , LYS B:338 , TRP B:459 , ALA B:460 , CAS B:470BINDING SITE FOR RESIDUE GOL B 805
21CC3SOFTWARESER B:556 , LYS B:557 , SER B:558BINDING SITE FOR RESIDUE GOL B 806
22CC4SOFTWAREARG B:719 , HOH B:1055BINDING SITE FOR RESIDUE GOL B 807
23CC5SOFTWARETRP B:685BINDING SITE FOR RESIDUE GOL B 808
24CC6SOFTWAREMET B:0 , GLU B:239 , TYR B:359 , PHE B:370 , ASP B:446BINDING SITE FOR RESIDUE GOL B 809
25CC7SOFTWAREARG B:408 , HOH B:973 , HOH B:1011 , HOH B:1012 , HOH B:1023 , HOH B:1067BINDING SITE FOR RESIDUE GOL B 810
26CC8SOFTWAREVAL B:473 , LEU B:478 , 0P6 B:812 , HOH B:1069 , HOH B:1070BINDING SITE FOR RESIDUE GOL B 811
27CC9SOFTWARETYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , GLU B:368 , VAL B:471 , TYR B:472 , VAL B:473 , ASP B:476 , GOL B:811 , HOH B:1105 , HOH B:1106BINDING SITE FOR RESIDUE 0P6 B 812

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Val A:428 -Pro A:429
2Phe A:508 -Pro A:509
3Ile A:658 -Pro A:659
4Val B:428 -Pro B:429
5Phe B:508 -Pro B:509
6Ile B:658 -Pro B:659

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG8)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG8)

(-) 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:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee..ee.........hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg8 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  |    477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 
                                                                                                                                                                                                                                                                  470-CAS                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains -----d4eg8b1 B:237-606 automated matches                                                                                                                                                                                                                                                                                                                                            d4eg8b2 B:607-767 automated matches                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeee....eeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee........eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg8 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       381|      394       404       414       424       434       444       454       464     | 474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764   
                                0|                                                                                                                                             381|                                                                                  470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              385
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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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  Q38C91_TRYB2 | Q38C91
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q38C91_TRYB2 | Q38C91: 5tqu
UniProtKB/TrEMBL
        Q38C91_TRYB2 | Q38C91: 4eg1 4eg3 4eg4 4eg5 4eg6 4eg7 4ega 4mvw 4mvx 4mvy 4mw0 4mw1 4mw2 4mw4 4mw5 4mw6 4mw7 4mw9 4mwb 4mwc 4mwd 4mwe 4zt2 4zt3 4zt4 4zt5 4zt6 4zt7 5j58 5j59 5j5a

(-) Related Entries Specified in the PDB File

4eg1 THE SAME PROTEIN IN COMPLEX WITH SUBSTRATE METHIONINE
4eg3 THE SAME PROTEIN IN COMPLEX WITH SUBSTRATE METHIONYL- ADENYLATE
4eg4 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1289
4eg5 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1312
4eg6 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1325
4eg7 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1331
4ega THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1320