spacer
spacer

PDBsum entry 3hu3

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
3hu3
Jmol PyMol
Contents
Protein chains
453 a.a. *
Ligands
AGS ×2
Metals
_MG ×2
Waters ×263
* Residue conservation analysis
PDB id:
3hu3
Name: Transport protein
Title: Structure of p97 n-d1 r155h mutant in complex with atpgs
Structure: Transitional endoplasmic reticulum atpase. Chain: a, b. Fragment: residues 1-481. Synonym: ter atpase, 15s mg(2+)-atpase p97 subunit, valosin containing protein, vcp. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: human. Gene: p97, vcp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.172     R-free:   0.193
Authors: W.-K.Tang
Key ref: W.K.Tang et al. (2010). A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants. EMBO J, 29, 2217-2229. PubMed id: 20512113
Date:
12-Jun-09     Release date:   16-Jun-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P55072  (TERA_HUMAN) -  Transitional endoplasmic reticulum ATPase
Seq:
Struc:
 
Seq:
Struc:
806 a.a.
453 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.6  - Vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
Bound ligand (Het Group name = AGS)
matches with 93.75% similarity
+ H(2)O
= ADP
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     ATP binding     1 term  

 

 
    reference    
 
 
EMBO J 29:2217-2229 (2010)
PubMed id: 20512113  
 
 
A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants.
W.K.Tang, D.Li, C.C.Li, L.Esser, R.Dai, L.Guo, D.Xia.
 
  ABSTRACT  
 
Mutations in p97, a major cytosolic AAA (ATPases associated with a variety of cellular activities) chaperone, cause inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). IBMPFD mutants have single amino-acid substitutions at the interface between the N-terminal domain (N-domain) and the adjacent AAA domain (D1), resulting in a reduced affinity for ADP. The structures of p97 N-D1 fragments bearing IBMPFD mutations adopt an atypical N-domain conformation in the presence of Mg(2+).ATPgammaS, which is reversible by ADP, showing for the first time the nucleotide-dependent conformational change of the N-domain. The transition from the ADP- to the ATPgammaS-bound state is accompanied by a loop-to-helix conversion in the N-D1 linker and by an apparent re-ordering in the N-terminal region of p97. X-ray scattering experiments suggest that wild-type p97 subunits undergo a similar nucleotide-dependent N-domain conformational change. We propose that IBMPFD mutations alter the timing of the transition between nucleotide states by destabilizing the ADP-bound form and consequently interfere with the interactions between the N-domains and their substrates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22298039 H.Meyer, M.Bug, and S.Bremer (2012).
Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system.
  Nat Cell Biol, 14, 117-123.  
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.  
21152665 E.Chapman, A.N.Fry, and M.Kang (2011).
The complexities of p97 function in health and disease.
  Mol Biosyst, 7, 700-710.  
21145000 J.O.Johnson, J.Mandrioli, M.Benatar, Y.Abramzon, V.M.Van Deerlin, J.Q.Trojanowski, J.R.Gibbs, M.Brunetti, S.Gronka, J.Wuu, J.Ding, L.McCluskey, M.Martinez-Lage, D.Falcone, D.G.Hernandez, S.Arepalli, S.Chong, J.C.Schymick, J.Rothstein, F.Landi, Y.D.Wang, A.Calvo, G.Mora, M.Sabatelli, M.R.Monsurrò, S.Battistini, F.Salvi, R.Spataro, P.Sola, G.Borghero, G.Galassi, S.W.Scholz, J.P.Taylor, G.Restagno, A.Chiò, B.J.Traynor, F.Giannini, C.Ricci, C.Moglia, I.Ossola, A.Canosa, S.Gallo, G.Tedeschi, P.Sola, I.Bartolomei, K.Marinou, L.Papetti, A.Conte, M.Luigetti, V.La Bella, P.Paladino, C.Caponnetto, P.Volanti, M.G.Marrosu, and M.R.Murru (2010).
Exome sequencing reveals VCP mutations as a cause of familial ALS.
  Neuron, 68, 857-864.  
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.

 

spacer

spacer