PDBsum entry 2pjh

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protein Protein-protein interface(s) links
Transport protein PDB id
Protein chains
76 a.a. *
193 a.a. *
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Strctural model of the p97 n domain- npl4 ubd complex
Structure: Nuclear protein localization protein 4 homolog. Chain: a. Fragment: n domain (residues 1-80). Synonym: protein npl4. Engineered: yes. Transitional endoplasmic reticulum atpase. Chain: b. Fragment: ubd (residues 21-213). Synonym: ter atpase, 15s mg2+, - atpase p97 subunit,
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: p97. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: npl4. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 1 models
Authors: R.Isaacson,V.E.Pye,S.Simpson,H.H.Meyer,X.Zhang,P.Freemont
Key ref:
R.L.Isaacson et al. (2007). Detailed structural insights into the p97-Npl4-Ufd1 interface. J Biol Chem, 282, 21361-21369. PubMed id: 17491009 DOI: 10.1074/jbc.M610069200
16-Apr-07     Release date:   08-May-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P60670  (NPL4_MOUSE) -  Nuclear protein localization protein 4 homolog
608 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
Q01853  (TERA_MOUSE) -  Transitional endoplasmic reticulum ATPase
806 a.a.
193 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain B: E.C.  - Vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


DOI no: 10.1074/jbc.M610069200 J Biol Chem 282:21361-21369 (2007)
PubMed id: 17491009  
Detailed structural insights into the p97-Npl4-Ufd1 interface.
R.L.Isaacson, V.E.Pye, P.Simpson, H.H.Meyer, X.Zhang, P.S.Freemont, S.Matthews.
The AAA ATPase, p97, achieves its versatility through binding to a wide range of cofactor proteins that adapt it to different cellular functions. The heterodimer UN (comprising Ufd1 and Npl4) is an adaptor complex that recruits p97 for numerous tasks, many of which involve the ubiquitin pathway. Insights into the structural specificity of p97 for its UN adaptor are currently negligible. Here, we present the solution structure of the Npl4 "ubiquitin-like" domain (UBD), which adopts a beta-grasp fold with a 3(10) helical insert. Moreover we performed a chemical shift perturbation analysis of its binding surface with the p97 N domain. We assigned the backbone amides of the p97 N domain and probed both its reciprocal binding surface with Npl4 UBD and its interaction with the p97-binding region of Ufd1. NMR data recorded on a 400-kDa full-length UN-hexamer p97 complex reveals an identical mode of interaction. We calculated a structural model for the p97 N-Npl4 UBD complex, and a comparison with the p97-p47 adaptor complex reveals subtle differences in p97 adaptor recognition and specificity.
  Selected figure(s)  
Figure 5.
FIGURE 5. HADDOCK-derived model for the Npl4 UBD-p97 N complex. A, C[ ]traces representing the super-position of the 10 refined Npl4 UBD-p97 N complex structures using the HADDOCK approach. B, ribbon representation of the Npl4 UBD (pink)-p97 N (blue) complex. C, ribbon representation of the p47 UBX (gold)-p97 N (blue) complex. The coordinates for the p47 UBX-p97 N complex are taken from PDB accession number 1S3S (20). D, close-up view of key interacting side chains shown in stick representation. E, close-up view of residues in Npl4 UBD, which, when mutated by Bruderer et al. (15), abolished binding to p97 N domain.
Figure 6.
FIGURE 6. Localization of the p97 N interaction motif within Ufd1. A, ^1H-^13C HSQC spectra of the specifically labeled Ufd1 (215-241) peptide (DHSGYAGEVGFRAFSGSGNRLDGKKKG, ^13C/^15N labels in bold and underlined) within increasing amounts of p97 N. B, sequence alignment of the Ufd1 peptide with p47 homologues illustrating the conserved nature of this motif.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 21361-21369) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21152665 E.Chapman, A.N.Fry, and M.Kang (2011).
The complexities of p97 function in health and disease.
  Mol Biosyst, 7, 700-710.  
19887446 C.Zhao, E.A.Matveeva, Q.Ren, and S.W.Whiteheart (2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
  J Biol Chem, 285, 761-772.  
  21103003 D.S.Haines (2010).
p97-containing complexes in proliferation control and cancer: emerging culprits or guilt by association?
  Genes Cancer, 1, 753-763.  
19805280 G.Zhao, G.Li, H.Schindelin, and W.J.Lennarz (2009).
An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation.
  Proc Natl Acad Sci U S A, 106, 16197-16202.
PDB code: 3gae
19497384 L.Madsen, M.Seeger, C.A.Semple, and R.Hartmann-Petersen (2009).
New ATPase regulators--p97 goes to the PUB.
  Int J Biochem Cell Biol, 41, 2380-2388.  
18656546 L.Madsen, K.M.Andersen, S.Prag, T.Moos, C.A.Semple, M.Seeger, and R.Hartmann-Petersen (2008).
Ubxd1 is a novel co-factor of the human p97 ATPase.
  Int J Biochem Cell Biol, 40, 2927-2942.  
18854144 T.R.Heallen, H.P.Adams, T.Furuta, K.J.Verbrugghe, and J.M.Schumacher (2008).
An Afg2/Spaf-related Cdc48-like AAA ATPase regulates the stability and activity of the C. elegans Aurora B kinase AIR-2.
  Dev Cell, 15, 603-616.  
18041839 R.L.Isaacson, P.J.Simpson, M.Liu, E.Cota, X.Zhang, P.Freemont, and S.Matthews (2007).
A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues.
  J Am Chem Soc, 129, 15428-15429.  
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 code is shown on the right.