4V8X

Structure of Thermus thermophilus ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.

Feng, S.Chen, Y.Kamada, K.Wang, H.Tang, K.Wang, M.Gao, Y.

(2013) Nucleic Acids Res 41: 9549

  • DOI: 10.1093/nar/gkt742
  • Primary Citation of Related Structures:  
    4V8X

  • PubMed Abstract: 
  • As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA ...

    As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'-phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.


    Organizational Affiliation

    School of Biological Science, Nanyang Technological University, 637551 Singapore, RIKEN Advanced Science Institute, Saitama 351-0198, Japan, Swiss Light Source, Paul Scherrer Institut, CH-5232, Switzerland and Institute of Molecular and Cell Biology, A-STAR, 138673, Singapore.



Macromolecules

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12AL, CL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXAU, CU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEMAY, AZ, CY, CZ84Escherichia coli K-12Mutation(s): 0 
Gene Names: B1563JW1555RELEyoeBb4539JW5331
EC: 3.1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33B6, D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6BH, DH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9BI, DI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16BQ, DQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10AJ, CJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11AK, CK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13AM, CM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZAN, CN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15AO, CO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16AP, CP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17AQ, CQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18AR, CR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19AS, CS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2AB, CB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20AT, CT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27B0, D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28B1, D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29B2, D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30B3, D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3AC, CC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31B4, D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32B5, D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34B7, D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35B8, D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36B9, D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1BC, DC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2BD, DD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4AD, CD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3BE, DE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4BF, DF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5BG, DG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L10BJ, DJ130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L13BN, DN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L14BO, DO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L15BP, DP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 5
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30S RIBOSOMAL PROTEIN S5AE, CE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 50
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50S RIBOSOMAL PROTEIN L17BR, DR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
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50S RIBOSOMAL PROTEIN L18BS, DS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 52
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50S RIBOSOMAL PROTEIN L19BT, DT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L20BU, DU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L21BV, DV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 55
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50S RIBOSOMAL PROTEIN L22BW, DW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 56
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50S RIBOSOMAL PROTEIN L23BX, DX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 57
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50S RIBOSOMAL PROTEIN L24BY, DY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25BZ, DZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6AF, CF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7AG, CG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8AH, CH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9AI, CI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsLengthOrganismImage
transfer RNAAV77Thermus thermophilus HB8
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  • Entity ID: 59
    MoleculeChainsLengthOrganismImage
    BACTERIAL TOXIN YOEBCX10Escherichia coli
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    Entity ID: 1
    MoleculeChainsLengthOrganismImage
    16S ribosomal RNAAA, CA1504Thermus thermophilus HB8
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    Entity ID: 23
    MoleculeChainsLengthOrganismImage
    transfer RNAAW, CV, CW77Thermus thermophilus HB8
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    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'AX25synthetic construct
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    Entity ID: 36
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNABA, DA2848Thermus thermophilus HB8
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    Entity ID: 37
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNABB, DB119Thermus thermophilus HB8
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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    AD, AN, CD, CN
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    AA, AL, AV, AX, B0, B1, B5, BA, BB, BF, BP, BX, CA, CG, CL, CV, D1, D5, DA, DB, DF, DR, DX
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.35 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.223 
    • R-Value Observed: 0.223 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 211.594α = 90
    b = 455.434β = 90
    c = 616.94γ = 90
    Software Package:
    Software NamePurpose
    CNSmodel building
    CNSrefinement
    CNSdata reduction
    CNSdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2016-07-27
      Changes: Derived calculations
    • Version 1.3: 2018-04-04
      Changes: Data collection, Source and taxonomy, Structure summary