4PK3

tubulin acetyltransferase complex with bisubstrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.347 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for age-dependent microtubule acetylation by tubulin acetyltransferase.

Szyk, A.Deaconescu, A.M.Spector, J.Goodman, B.Valenstein, M.L.Ziolkowska, N.E.Kormendi, V.Grigorieff, N.Roll-Mecak, A.

(2014) Cell 157: 1405-1415

  • DOI: 10.1016/j.cell.2014.03.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acetylation of α-tubulin Lys40 by tubulin acetyltransferase (TAT) is the only known posttranslational modification in the microtubule lumen. It marks stable microtubules and is required for polarity establishment and directional migration. Here, we e ...

    Acetylation of α-tubulin Lys40 by tubulin acetyltransferase (TAT) is the only known posttranslational modification in the microtubule lumen. It marks stable microtubules and is required for polarity establishment and directional migration. Here, we elucidate the mechanistic underpinnings for TAT activity and its preference for microtubules with slow turnover. 1.35 Å TAT cocrystal structures with bisubstrate analogs constrain TAT action to the microtubule lumen and reveal Lys40 engaged in a suboptimal active site. Assays with diverse tubulin polymers show that TAT is stimulated by microtubule interprotofilament contacts. Unexpectedly, despite the confined intraluminal location of Lys40, TAT efficiently scans the microtubule bidirectionally and acetylates stochastically without preference for ends. First-principles modeling and single-molecule measurements demonstrate that TAT catalytic activity, not constrained luminal diffusion, is rate limiting for acetylation. Thus, because of its preference for microtubules over free tubulin and its modest catalytic rate, TAT can function as a slow clock for microtubule lifetimes.


    Organizational Affiliation

    Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-tubulin N-acetyltransferase 1
A
198Homo sapiensMutation(s): 0 
Gene Names: ATAT1 (C6orf134, MEC17)
EC: 2.3.1.108
Find proteins for Q5SQI0 (Homo sapiens)
Go to Gene View: ATAT1
Go to UniProtKB:  Q5SQI0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACETYL-SER-ASP-(N-ACETYL-LYS)-THR-NH2 PEPTIDE
B
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.347 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.163α = 90.00
b = 52.284β = 107.13
c = 50.142γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited States1ZIANS003122

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary