5NYW

Anbu (ancestral beta-subunit) from Yersinia bercovieri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers.

Piasecka, A.Czapinska, H.Vielberg, M.T.Szczepanowski, R.H.Kiefersauer, R.Reed, S.Groll, M.Bochtler, M.

(2018) J. Mol. Biol. 430: 611-627

  • DOI: 10.1016/j.jmb.2017.11.016

  • PubMed Abstract: 
  • Ancestral β-subunit (Anbu) is homologous to HslV and 20S proteasomes. Based on its phylogenetic distribution and sequence clustering, Anbu has been proposed as the "ancestral" form of proteasomes. Here, we report biochemical data, small-angle X-ray s ...

    Ancestral β-subunit (Anbu) is homologous to HslV and 20S proteasomes. Based on its phylogenetic distribution and sequence clustering, Anbu has been proposed as the "ancestral" form of proteasomes. Here, we report biochemical data, small-angle X-ray scattering results, negative-stain electron microscopy micrographs and a crystal structure of the Anbu particle from Yersinia bercovieri (YbAnbu). All data are consistent with YbAnbu forming defined 12-14 subunit multimers that differ in shape from both HslV and 20S proteasomes. The crystal structure reveals that YbAnbu subunits form tight dimers, held together in part by the Anbu specific C-terminal helices. These dimers ("protomers") further assemble into a low-rise left-handed staircase. The lock-washer shape of YbAnbu is consistent with the presence of defined multimers, X-ray diffraction data in solution and negative-stain electron microscopy images. The presented structure suggests a possible evolutionary pathway from helical filaments to highly symmetric or pseudosymmetric multimer structures. YbAnbu subunits have the Ntn-hydrolase fold, a putative S1 pocket and conserved candidate catalytic residues Thr1, Asp17 and Lys32(33). Nevertheless, we did not detect any YbAnbu peptidase or amidase activity. However, we could document orthophosphate production from ATP catalyzed by the ATP-grasp protein encoded in the Y. bercovieri Anbu operon.


    Organizational Affiliation

    Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland; School of Medicine, Cardiff University, Cardiff, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2
251N/AMutation(s): 2 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
1, 2, A, B, E, L, P, V, W, X, Z
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
1, C, D, G, K, L, M, P, Q, R, S, T, U, W, Z
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C, D, F, K, L, O
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UNK
Query on UNK

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Download CCD File 
I, Q, U
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
 Ligand Interaction
AZI
Query on AZI

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J
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
N, T
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.535α = 90.00
b = 285.371β = 91.78
c = 179.213γ = 90.00
Software Package:
Software NamePurpose
ARP/wARPphasing
PHENIXrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CentrePolandNCN UMO-2013/08/S/NZ1/00681
Cardiff UniversityUnited Kingdom--

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Refinement description
  • Version 1.2: 2018-01-03
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Database references