Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.26 kDa 
• Atom Count: 642 
• Modelled Residue Count: 77 
• Deposited Residue Count: 78 
• Unique protein chains: 1

2RPA

The solution structure of N-terminal domain of microtubule severing enzyme

• PDB DOI: 10.2210/pdb2RPA/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-05-13 Released: 2009-05-26 
• Deposition Author(s): Iwaya, N., Kuwahara, Y., Unzai, S., Nagata, T., Tomii, K., Goda, N., Tochio, H., Shirakawa, M., Hiroaki, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

A common substrate recognition mode conserved between katanin P60 and VPS4 governs microtubule severing and membrane skeleton reorganization

Iwaya, N., Kuwahara, Y., Fujiwara, Y., Goda, N., Tenno, T., Akiyama, K., Mase, S., Tochio, H., Ikegami, T., Shirakawa, M., Hiroaki, H.

(2010) J Biol Chem 285: 16822-16829

• PubMed: 20339000 
• DOI: 10.1074/jbc.M110.108365
• Primary Citation of Related Structures:  
  2RPA


• PubMed Abstract: 
  

Katanin p60 (kp60), a microtubule-severing enzyme, plays a key role in cytoskeletal reorganization during various cellular events in an ATP-dependent manner. We show that a single domain isolated from the N terminus of mouse katanin p60 (kp60-NTD) binds to tubulin. The solution structure of kp60-NTD was determined by NMR. Although their sequence similarities were as low as 20%, the structure of kp60-NTD revealed a striking similarity to those of the microtubule interacting and trafficking (MIT) domains, which adopt anti-parallel three-stranded helix bundle. In particular, the arrangement of helices 2 and 3 is well conserved between kp60-NTD and the MIT domain from Vps4, which is a homologous protein that promotes disassembly of the endosomal sorting complexes required for transport III membrane skeleton complex. Mutation studies revealed that the positively charged surface formed by helices 2 and 3 binds tubulin. This binding mode resembles the interaction between the MIT domain of Vps4 and Vps2/CHMP1a, a component of endosomal sorting complexes required for transport III. Our results show that both the molecular architecture and the binding modes are conserved between two AAA-ATPases, kp60 and Vps4. A common mechanism is evolutionarily conserved between two distinct cellular events, one that drives microtubule severing and the other involving membrane skeletal reorganization.

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Organizational Affiliation: 

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8530, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Katanin p60 ATPase-containing subunit A1	A	78	Mus musculus	Mutation(s): 0  Gene Names: Katna1 EC: 3.6.4.3 (PDB Primary Data), 5.6.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WV86 (Mus musculus) Explore Q9WV86  Go to UniProtKB:  Q9WV86
IMPC:  MGI:1344353

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2RPA Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-13 
• Released Date: 2009-05-26 
Deposition Author(s): Iwaya, N., Kuwahara, Y., Unzai, S., Nagata, T., Tomii, K., Goda, N., Tochio, H., Shirakawa, M., Hiroaki, H.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations