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PDBsum entry 1r7r
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Transport protein PDB id
1r7r

 

 

 

 

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Contents
Protein chain
683 a.a. *
Ligands
ADP
* Residue conservation analysis
PDB id:
1r7r
Name: Transport protein
Title: The crystal structure of murine p97/vcp at 3.6a
Structure: Transitional endoplasmic reticulum atpase. Chain: a. Synonym: ter atpase, 15s mg(2+)-atpase p97 subunit, valosin containing protein, vcp. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: vcp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
3.60Å     R-factor:   0.327     R-free:   0.358
Authors: T.Huyton,V.E.Pye,L.C.Briggs,T.C.Flynn,F.Beuron,H.Kondo,J.Ma,X.Zhang, P.S.Freemont
Key ref: T.Huyton et al. (2003). The crystal structure of murine p97/VCP at 3.6A. J Struct Biol, 144, 337-348. PubMed id: 14643202 DOI: 10.1016/j.jsb.2003.10.007
Date:
22-Oct-03     Release date:   16-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q01853  (TERA_MOUSE) -  Transitional endoplasmic reticulum ATPase from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		806 a.a.
683 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.6  - vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 =
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/j.jsb.2003.10.007 J Struct Biol 144:337-348 (2003)
PubMed id: 14643202  
 
 
The crystal structure of murine p97/VCP at 3.6A.
T.Huyton, V.E.Pye, L.C.Briggs, T.C.Flynn, F.Beuron, H.Kondo, J.Ma, X.Zhang, P.S.Freemont.
 
  ABSTRACT  
 
p97/VCP is a member of the AAA ATPase family and has roles in both membrane fusion and ubiquitin dependent protein degradation. Here, we present a 3.6A crystal structure of murine p97 in which D2 domain has been modelled as poly-alanine and the remaining approximately 100 residues are absent. The resulting structure illustrates a head-to-tail packing arrangement of the two p97 AAA domains in a natural hexameric state with D1 ADP bound and D2 nucleotide free. The head-to-tail packing arrangement observed in this structure is in contrast to our previously predicted tail-to-tail packing model. The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22307055 L.F.Chang, S.Chen, C.C.Liu, X.Pan, J.Jiang, X.C.Bai, X.Xie, H.W.Wang, and S.F.Sui (2012).
Structural characterization of full-length NSF and 20S particles.
  Nat Struct Mol Biol, 19, 268-275.  
21383145 T.F.Chou, S.J.Brown, D.Minond, B.E.Nordin, K.Li, A.C.Jones, P.Chase, P.R.Porubsky, B.M.Stoltz, F.J.Schoenen, M.P.Patricelli, P.Hodder, H.Rosen, and R.J.Deshaies (2011).
Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways.
  Proc Natl Acad Sci U S A, 108, 4834-4839.  
20130678 C.A.Ewens, P.Kloppsteck, A.Förster, X.Zhang, and P.S.Freemont (2010).
Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97.
  Biochem Cell Biol, 88, 41-48.  
  21103003 D.S.Haines (2010).
p97-containing complexes in proliferation control and cancer: emerging culprits or guilt by association?
  Genes Cancer, 1, 753-763.  
21098306 I.Stokes-Rees, and P.Sliz (2010).
Protein structure determination by exhaustive search of Protein Data Bank derived databases.
  Proc Natl Acad Sci U S A, 107, 21476-21481.  
20130682 P.Wendler, and H.R.Saibil (2010).
Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?
  Biochem Cell Biol, 88, 89-96.  
20130680 T.Haslberger, B.Bukau, and A.Mogk (2010).
Towards a unifying mechanism for ClpB/Hsp104-mediated protein disaggregation and prion propagation.
  Biochem Cell Biol, 88, 63-75.  
20512113 W.K.Tang, D.Li, C.C.Li, L.Esser, R.Dai, L.Guo, and D.Xia (2010).
A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants.
  EMBO J, 29, 2217-2229.
PDB codes: 3hu1 3hu2 3hu3
19171967 A.T.Brunger, B.Delabarre, J.M.Davies, and W.I.Weis (2009).
X-ray structure determination at low resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 128-133.  
19361443 G.Effantin, R.Rosenzweig, M.H.Glickman, and A.C.Steven (2009).
Electron microscopic evidence in support of alpha-solenoid models of proteasomal subunits Rpn1 and Rpn2.
  J Mol Biol, 386, 1204-1211.  
19278657 M.J.Landsberg, P.R.Vajjhala, R.Rothnagel, A.L.Munn, and B.Hankamer (2009).
Three-dimensional structure of AAA ATPase Vps4: advancing structural insights into the mechanisms of endosomal sorting and enveloped virus budding.
  Structure, 17, 427-437.  
19818707 R.Ernst, B.Mueller, H.L.Ploegh, and C.Schlieker (2009).
The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER.
  Mol Cell, 36, 28-38.  
  19923742 W.K.Tang, D.Li, L.Esser, and D.Xia (2009).
Purification, crystallization and preliminary X-ray diffraction analysis of disease-related mutants of p97.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1166-1170.  
18650442 C.Cho, S.L.Reck-Peterson, and R.D.Vale (2008).
Regulatory ATPase sites of cytoplasmic dynein affect processivity and force generation.
  J Biol Chem, 283, 25839-25845.  
18462676 J.M.Davies, A.T.Brunger, and W.I.Weis (2008).
Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
  Structure, 16, 715-726.
PDB codes: 3cf0 3cf1 3cf2 3cf3
18332143 L.C.Briggs, G.S.Baldwin, N.Miyata, H.Kondo, X.Zhang, and P.S.Freemont (2008).
Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase.
  J Biol Chem, 283, 13745-13752.  
18929572 M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, and C.P.Hill (2008).
Biochemical and structural studies of yeast Vps4 oligomerization.
  J Mol Biol, 384, 878-895.
PDB codes: 3eie 3eih
18280501 Z.Yu, M.D.Gonciarz, W.I.Sundquist, C.P.Hill, and G.J.Jensen (2008).
Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p.
  J Mol Biol, 377, 364-377.  
17397838 C.Zhao, J.T.Slevin, and S.W.Whiteheart (2007).
Cellular functions of NSF: not just SNAPs and SNAREs.
  FEBS Lett, 581, 2140-2149.  
17394253 M.Kavoosi, A.L.Creagh, D.G.Kilburn, and C.A.Haynes (2007).
Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed in Escherichia coli.
  Biotechnol Bioeng, 98, 599-610.  
18160044 P.Wendler, J.Shorter, C.Plisson, A.G.Cashikar, S.Lindquist, and H.R.Saibil (2007).
Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
  Cell, 131, 1366-1377.  
17491009 R.L.Isaacson, V.E.Pye, P.Simpson, H.H.Meyer, X.Zhang, P.S.Freemont, and S.Matthews (2007).
Detailed structural insights into the p97-Npl4-Ufd1 interface.
  J Biol Chem, 282, 21361-21369.
PDB code: 2pjh
17244533 S.Lee, J.M.Choi, and F.T.Tsai (2007).
Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB.
  Mol Cell, 25, 261-271.  
17202270 V.E.Pye, F.Beuron, C.A.Keetch, C.McKeown, C.V.Robinson, H.H.Meyer, X.Zhang, and P.S.Freemont (2007).
Structural insights into the p97-Ufd1-Npl4 complex.
  Proc Natl Acad Sci U S A, 104, 467-472.  
16855310 B.DeLaBarre, and A.T.Brunger (2006).
Considerations for the refinement of low-resolution crystal structures.
  Acta Crystallogr D Biol Crystallogr, 62, 923-932.  
16713576 B.DeLaBarre, J.C.Christianson, R.R.Kopito, and A.T.Brunger (2006).
Central pore residues mediate the p97/VCP activity required for ERAD.
  Mol Cell, 22, 451-462.  
  17379943 C.Hicks-Berger, I.Sokolchik, C.Kim, and D.J.Morré (2006).
A plasma membrane-associated AAA-ATPase from Glycine max.
  Biofactors, 28, 135-149.  
  17379941 D.J.Morré, C.Kim, and C.Hicks-Berger (2006).
ATP-dependent and drug-inhibited vesicle enlargement reconstituted using synthetic lipids and recombinant proteins.
  Biofactors, 28, 105-117.  
16601695 F.Beuron, I.Dreveny, X.Yuan, V.E.Pye, C.McKeown, L.C.Briggs, M.J.Cliff, Y.Kaneko, R.Wallis, R.L.Isaacson, J.E.Ladbury, S.J.Matthews, H.Kondo, X.Zhang, and P.S.Freemont (2006).
Conformational changes in the AAA ATPase p97-p47 adaptor complex.
  EMBO J, 25, 1967-1976.  
16709668 G.Li, G.Zhao, X.Zhou, H.Schindelin, and W.J.Lennarz (2006).
The AAA ATPase p97 links peptide N-glycanase to the endoplasmic reticulum-associated E3 ligase autocrine motility factor receptor.
  Proc Natl Acad Sci U S A, 103, 8348-8353.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
16430918 M.Rappas, J.Schumacher, H.Niwa, M.Buck, and X.Zhang (2006).
Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.
  J Mol Biol, 357, 481-492.
PDB codes: 2c96 2c98 2c99 2c9c
16236712 A.Gerega, B.Rockel, J.Peters, T.Tamura, W.Baumeister, and P.Zwickl (2005).
VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase.
  J Biol Chem, 280, 42856-42862.  
15698559 B.Nagar, and J.Kuriyan (2005).
SAXS and the working protein.
  Structure, 13, 169-170.  
15652483 H.Richly, M.Rape, S.Braun, S.Rumpf, C.Hoege, and S.Jentsch (2005).
A series of ubiquitin binding factors connects CDC48/p97 to substrate multiubiquitylation and proteasomal targeting.
  Cell, 120, 73-84.  
15698563 J.M.Davies, H.Tsuruta, A.P.May, and W.I.Weis (2005).
Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering.
  Structure, 13, 183-195.  
16056265 S.Elsasser, and D.Finley (2005).
Delivery of ubiquitinated substrates to protein-unfolding machines.
  Nat Cell Biol, 7, 742-749.  
15498773 D.M.Rancour, S.Park, S.D.Knight, and S.Y.Bednarek (2004).
Plant UBX domain-containing protein 1, PUX1, regulates the oligomeric structure and activity of arabidopsis CDC48.
  J Biol Chem, 279, 54264-54274.  
14988733 I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, and P.S.Freemont (2004).
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
  EMBO J, 23, 1030-1039.
PDB code: 1s3s
15328346 K.Shiozawa, N.Maita, K.Tomii, A.Seto, N.Goda, Y.Akiyama, T.Shimizu, M.Shirakawa, and H.Hiroaki (2004).
Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain.
  J Biol Chem, 279, 50060-50068.
PDB code: 1wlf
15371428 R.M.Bruderer, C.Brasseur, and H.H.Meyer (2004).
The AAA ATPase p97/VCP interacts with its alternative co-factors, Ufd1-Npl4 and p47, through a common bipartite binding mechanism.
  J Biol Chem, 279, 49609-49616.  
15556993 S.L.Kazmirski, M.Podobnik, T.F.Weitze, M.O'Donnell, and J.Kuriyan (2004).
Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex.
  Proc Natl Acad Sci U S A, 101, 16750-16755.
PDB codes: 1xxh 1xxi
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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