4V9R

Crystal structure of antibiotic DITYROMYCIN bound to 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Literature

The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.

Bulkley, D.Brandi, L.Polikanov, Y.S.Fabbretti, A.O'Connor, M.Gualerzi, C.O.Steitz, T.A.

(2014) Cell Rep 6: 357-365

  • DOI: 10.1016/j.celrep.2013.12.024
  • Primary Citation of Related Structures:  
    4V9R, 4V9S

  • PubMed Abstract: 
  • The translocation of mRNA and tRNA through the ribosome is catalyzed by elongation factor G (EF-G), a universally conserved guanosine triphosphate hydrolase (GTPase). The mechanism by which the closely related decapeptide antibiotics dityromycin and GE82832 inhibit EF-G-catalyzed translocation is elucidated in this study ...

    The translocation of mRNA and tRNA through the ribosome is catalyzed by elongation factor G (EF-G), a universally conserved guanosine triphosphate hydrolase (GTPase). The mechanism by which the closely related decapeptide antibiotics dityromycin and GE82832 inhibit EF-G-catalyzed translocation is elucidated in this study. Using crystallographic and biochemical experiments, we demonstrate that these antibiotics bind to ribosomal protein S12 in solution alone as well as within the small ribosomal subunit, inducing long-range effects on the ribosomal head. The crystal structure of the antibiotic in complex with the 70S ribosome reveals that the binding involves conserved amino acid residues of S12 whose mutations result in in vitro and in vivo antibiotic resistance and loss of antibiotic binding. The data also suggest that GE82832/dityromycin inhibits EF-G-catalyzed translocation by disrupting a critical contact between EF-G and S12 that is required to stabilize the posttranslocational conformation of EF-G, thereby preventing the ribosome-EF-G complex from entering a conformation productive for translocation.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, New Haven, CT 06511, USA. Electronic address: thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S2B [auth AB],
EB [auth CB]
256Thermus thermophilusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S3C [auth AC],
FB [auth CC]
239Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S4D [auth AD],
GB [auth CD]
209Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S5E [auth AE],
HB [auth CE]
162Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S6F [auth AF],
IB [auth CF]
101Thermus thermophilusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S7G [auth AG],
JB [auth CG]
156Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S8H [auth AH],
KB [auth CH]
138Thermus thermophilusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S9I [auth AI],
LB [auth CI]
128Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S10J [auth AJ],
MB [auth CJ]
105Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S11K [auth AK],
NB [auth CK]
129Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S12L [auth AL],
OB [auth CL]
132Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S13M [auth AM],
PB [auth CM]
126Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S14N [auth AN],
QB [auth CN]
61Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S15O [auth AO],
RB [auth CO]
89Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S16P [auth AP],
SB [auth CP]
88Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S17Q [auth AQ],
TB [auth CQ]
105Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S18R [auth AR],
UB [auth CR]
88Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S19S [auth AS],
VB [auth CS]
93Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S20T [auth AT],
WB [auth CT]
106Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein THXU [auth AU],
XB [auth CU]
27Thermus thermophilusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
DityromycinX [auth AW],
AC [auth CW]
10Streptomyces sp.Mutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L2AA [auth BD],
DC [auth DD]
276Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L3BA [auth BE],
EC [auth DE]
206Thermus thermophilusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L4CA [auth BF],
FC [auth DF]
210Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L5DA [auth BG],
GC [auth DG]
182Thermus thermophilusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L6EA [auth BH],
HC [auth DH]
180Thermus thermophilusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L9FA [auth BI],
IC [auth DI]
148Thermus thermophilusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L13GA [auth BN],
JC [auth DN]
140Thermus thermophilusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L14HA [auth BO],
KC [auth DO]
122Thermus thermophilusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L15IA [auth BP],
LC [auth DP]
150Thermus thermophilusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L16JA [auth BQ],
MC [auth DQ]
141Thermus thermophilusMutation(s): 0 
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Entity ID: 37
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50S Ribosomal Protein L17KA [auth BR],
NC [auth DR]
118Thermus thermophilusMutation(s): 0 
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Entity ID: 38
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50S Ribosomal Protein L18LA [auth BS],
OC [auth DS]
112Thermus thermophilusMutation(s): 0 
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Entity ID: 39
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50S Ribosomal Protein L19MA [auth BT],
PC [auth DT]
146Thermus thermophilusMutation(s): 0 
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Entity ID: 40
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50S Ribosomal Protein L20NA [auth BU],
QC [auth DU]
118Thermus thermophilusMutation(s): 0 
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Entity ID: 41
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50S Ribosomal Protein L21OA [auth BV],
RC [auth DV]
101Thermus thermophilusMutation(s): 0 
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Entity ID: 42
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50S Ribosomal Protein L22PA [auth BW],
SC [auth DW]
113Thermus thermophilusMutation(s): 0 
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Entity ID: 43
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50S Ribosomal Protein L23QA [auth BX],
TC [auth DX]
96Thermus thermophilusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L24RA [auth BY],
UC [auth DY]
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXrpl24
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Entity ID: 45
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50S Ribosomal Protein L25SA [auth BZ],
VC [auth DZ]
206Thermus thermophilusMutation(s): 0 
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Entity ID: 46
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50S Ribosomal Protein L27TA [auth B0],
WC [auth D0]
85Thermus thermophilusMutation(s): 0 
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Entity ID: 47
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50S Ribosomal Protein L28UA [auth B1],
XC [auth D1]
98Thermus thermophilusMutation(s): 0 
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Entity ID: 48
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50S Ribosomal Protein L29VA [auth B2],
YC [auth D2]
72Thermus thermophilusMutation(s): 0 
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UniProt GroupQ5SHP6
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L30WA [auth B3],
ZC [auth D3]
60Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L31XA [auth B4],
AD [auth D4]
71Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L32YA [auth B5],
BD [auth D5]
60Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L33ZA [auth B6],
CD [auth D6]
54Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L34AB [auth B7],
DD [auth D7]
49Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L35BB [auth B8],
ED [auth D8]
65Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L36CB [auth B9],
FD [auth D9]
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJrpl36
UniProt
Find proteins for P80256 (Thermus thermophilus)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAA [auth AA],
DB [auth CA]
1,522Thermus thermophilus
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Entity ID: 22
MoleculeChainsLengthOrganismImage
mRNAV [auth AV],
YB [auth CV]
24N/A
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Entity ID: 23
MoleculeChainsLengthOrganismImage
P-site tRNAW [auth AX],
ZB [auth CX]
77Escherichia coli
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Entity ID: 25
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAY [auth BA],
BC [auth DA]
2,915Thermus thermophilus
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Entity ID: 26
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAZ [auth BB],
CC [auth DB]
122Thermus thermophilus
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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UL [auth AD],
ZZA [auth CD]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FME
Query on FME

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FM [auth AX],
GAB [auth CX]
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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ATA [auth B6],
CM [auth AN],
DAB [auth CN],
HTA [auth B9],
JSA [auth BY],
ATA [auth B6],
CM [auth AN],
DAB [auth CN],
HTA [auth B9],
JSA [auth BY],
LBC [auth DY],
OBC [auth D4],
RBC [auth D5],
SBC [auth D6],
UBC [auth D9],
XSA [auth B4],
YSA [auth B5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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GY [auth BA],
JJB [auth DA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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