Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors.


Abstract

The AAA+ ATPase p97 regulates ubiquitin-dependent protein homeostasis and has been pursued as a cancer drug target. The ATP-competitive inhibitor CB-5083 and allosteric inhibitor NMS-873 are the most advanced p97 inhibitors described to date. Previous studies have reported that their cytotoxicity can be readily overcome and involves single p97 mutations in the linker between the D1 and D2 ATPase domains and within D2. We report here that the proline 472 to leucine (P472L) mutation, in the D1-D2 linker and identified in CB-5083-resistant cells, desensitizes p97 to both inhibitor classes. This mutation does not disrupt the distinct D2-binding sites of the inhibitors. Instead, P472L changes ATPase domain communication within the p97 hexamer. P472L enhances cooperative D2 ATP binding and hydrolysis. This mechanism alters the function of the D1-D2 linker in the control of D2 activity involving the ATP-bound state of D1. Although increased D2 activity is sufficient to desensitize the P472L mutant to NMS-873, the mutant's desensitization to CB-5083 also requires D1 ATPase domain function. Our study highlights the remarkable adaptability of p97 ATPase domain communication that enables escape from mechanistically distinct classes of cytotoxic p97 inhibitors.

Submission Details

ID: btD9qUb7

Submitter: Shu-Ching Ou

Submission Date: March 7, 2019, 11:32 a.m.

Version: 1

Publication Details
Wei Y;Toth JI;Blanco GA;Bobkov AA;Petroski MD,J Biol Chem (2018) Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. PMID:30381397
Additional Information

ND means not determined.

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
2PJH 2007-05-08 Strctural Model of the p97 N domain- npl4 UBD complex
5B6C 2017-01-04 1.55 Structural Details of Ufd1 binding to p97
3TIW 2011-09-14 1.8 Crystal structure of p97N in complex with the C-terminus of gp78
4KDL 2014-03-19 1.81 Crystal structure of p97/VCP N in complex with OTU1 UBXL
4KDI 2014-03-19 1.86 Crystal structure of p97/VCP N in complex with OTU1 UBXL
5EPP 2016-09-14 1.88 Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4
3EBB 2009-02-24 1.9 PLAP/P97 complex
6G2V 2019-04-10 1.9 Crystal structure of the p97 D2 domain in a helical split-washer conformation
6G2Z 2019-04-10 1.92 Crystal structure of the p97 D2 domain in a helical split-washer conformation
4KO8 2013-11-13 1.98 Structure of p97 N-D1 R155H mutant in complex with ATPgS
3QQ8 2011-06-22 2.0 Crystal structure of p97-N in complex with FAF1-UBX
3QWZ 2012-05-09 2.0 Crystal structure of FAF1 UBX-p97N-domain complex
6G2X 2019-04-10 2.08 Crystal structure of the p97 D2 domain in a helical split-washer conformation
6G2Y 2019-04-10 2.15 Crystal structure of the p97 D2 domain in a helical split-washer conformation
5DYG 2016-02-10 2.2 Structure of p97 N-D1 L198W mutant in complex with ADP
3QC8 2011-07-20 2.2 Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change
3HU3 2010-06-16 2.2 Structure of p97 N-D1 R155H mutant in complex with ATPgS
5GLF 2016-11-09 2.25 Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease
5FTJ 2016-01-27 2.3 Cryo-EM structure of human p97 bound to UPCDC30245 inhibitor
4P0A 2014-05-07 2.3 Crystal structure of HOIP PUB domain in complex with p97 PIM
5FTK 2016-01-27 2.4 Cryo-EM structure of human p97 bound to ADP
5X4L 2017-03-22 2.4 Crystal structure of the UBX domain of human UBXD7 in complex with p97 N domain
6G30 2019-04-10 2.42 Crystal structure of the p97 D2 domain in a helical split-washer conformation
5IFS 2016-10-26 2.46 Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death
4KLN 2013-11-13 2.62 Structure of p97 N-D1 A232E mutant in complex with ATPgS
3QQ7 2011-06-22 2.65 Crystal Structure of the p97 N-terminal domain
6G2W 2019-04-10 2.68 Crystal structure of the p97 D2 domain in a helical split-washer conformation
5KIY 2017-12-20 2.79 p97 ND1-A232E in complex with VIMP
3HU1 2010-06-16 2.81 Structure of p97 N-D1 R95G mutant in complex with ATPgS
3HU2 2010-06-16 2.85 Structure of p97 N-D1 R86A mutant in complex with ATPgS
1E32 2001-05-31 2.9 Structure of the N-Terminal domain and the D1 AAA domain of membrane fusion ATPase p97
1S3S 2004-03-30 2.9 Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C
4KOD 2013-11-13 2.96 Structure of p97 N-D1 R155H mutant in complex with ADP
3CF0 2008-04-22 3.0 Structure of D2 subdomain of P97/VCP in complex with ADP
5C1B 2016-01-13 3.08 p97-delta709-728 in complex with a UFD1-SHP peptide
5FTM 2016-01-27 3.2 Cryo-EM structure of human p97 bound to ATPgS (Conformation II)
5FTL 2016-01-27 3.3 Cryo-EM structure of human p97 bound to ATPgS (Conformation I)
5C18 2016-01-13 3.3 p97-delta709-728 in complex with ATP-gamma-S
5FTN 2016-01-27 3.3 Cryo-EM structure of human p97 bound to ATPgS (Conformation III)
5IFW 2016-10-26 3.4 Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death
5KIW 2018-03-07 3.41 p97 ND1-L198W in complex with VIMP
3CF2 2008-04-22 3.5 Structure of P97/vcp in complex with ADP/AMP-PNP
1R7R 2003-12-16 3.6 The crystal structure of murine p97/VCP at 3.6A
5DYI 2016-02-10 3.71 Structure of p97 N-D1 wild-type in complex with ADP
6HD0 2019-08-28 3.73 Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
6MCK 2019-01-23 3.77 p97 D1D2 with CB5083 bound
5C1A 2016-01-13 3.8 p97-N750D/R753D/M757D/Q760D in complex with ATP-gamma-S
5C19 2016-01-13 4.2 p97 variant 2 in the apo state
3CF3 2008-04-22 4.25 Structure of P97/vcp in complex with ADP
3CF1 2008-04-22 4.4 Structure of P97/vcp in complex with ADP/ADP.alfx

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
600.0 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase P55072 TERA_HUMAN
600.0 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase Q01853 TERA_MOUSE
599.4 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase P46462 TERA_RAT
598.8 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase Q3ZBT1 TERA_BOVIN
598.8 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase P03974 TERA_PIG
576.0 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase Q6GL04 TERA_XENTR
573.0 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase P23787 TERA_XENLA
584.4 A,B,C,D,E,F Transitional endoplasmic reticulum ATPase Q7ZU99 TERA_DANRE