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PDBsum entry 1tr4

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protein links
Unknown function PDB id
1tr4
Jmol
Contents
Protein chain
226 a.a. *
* Residue conservation analysis
PDB id:
1tr4
Name: Unknown function
Title: Solution structure of human oncogenic protein gankyrin
Structure: 26s proteasome non-atpase regulatory subunit 10. Chain: a. Synonym: 26s proteasome regulatory subunit p28, gankyrin. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: psmd10. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 20 models
Authors: C.Yuan,J.Li,A.Mahajan,M.J.Poi,I.J.Byeon,M.D.Tsai
Key ref:
C.Yuan et al. (2004). Solution structure of the human oncogenic protein gankyrin containing seven ankyrin repeats and analysis of its structure--function relationship. Biochemistry, 43, 12152-12161. PubMed id: 15379554 DOI: 10.1021/bi049116o
Date:
19-Jun-04     Release date:   16-Nov-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
O75832  (PSD10_HUMAN) -  26S proteasome non-ATPase regulatory subunit 10
Seq:
Struc:
226 a.a.
226 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     proteasome complex   8 terms 
  Biological process     viral reproduction   32 terms 
  Biochemical function     protein binding     2 terms  

 

 
DOI no: 10.1021/bi049116o Biochemistry 43:12152-12161 (2004)
PubMed id: 15379554  
 
 
Solution structure of the human oncogenic protein gankyrin containing seven ankyrin repeats and analysis of its structure--function relationship.
C.Yuan, J.Li, A.Mahajan, M.J.Poi, I.J.Byeon, M.D.Tsai.
 
  ABSTRACT  
 
Human gankyrin (226 residues, 24.4 kDa) is a liver oncoprotein that plays an important role in the development of human hepatocellular carcinomas. In this paper, its solution structure is reported, which is the largest ankyrin protein ever determined by NMR. The highly degenerate primary sequences of the seven ankyrin repeats presented a major challenge, which was overcome by combined use of TROSY experiments, perdeuterated samples, isotope-filtered NMR experiments, and residual dipolar couplings. The final structure was of high quality, with atomic rmsds for the backbone (N, C', and C(alpha)) and all heavy atoms (residues 4-224) of 0.69 +/- 0.09 and 1.04 +/- 0.09 A, respectively. Detailed analyses of NMR data suggested that the conserved TPLH motifs play important structural roles in stabilizing the repeating ankyrin scaffold. Gankyrin is conformationally more stable than the tumor suppressor p16(INK4A), possibly due to the structural roles of conserved residues evidenced by slowly exchanging backbone amides as well as hydrogen bonding networks involving labile side chain protons. Structural comparison with p16(INK4A) identified several residues of gankyrin that are potentially important for CDK4 binding, whereas observation of the thiol proton of C180 indicated a well-structured Rb-binding site in the helical region of the sixth ankyrin repeat. Interestingly, the CDK4-binding site and Rb-binding site located in N- and C-terminal regions, respectively, are separated by comparatively more stable ankyrin repeats and highly condensed positive surface charge. These results and analyses will shed light on the structural basis of the function of human gankyrin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17935131 C.M.Ortiz, T.Ito, E.Tanaka, S.Tsunoda, S.Nagayama, Y.Sakai, H.Higashitsuji, J.Fujita, and Y.Shimada (2008).
Gankyrin oncoprotein overexpression as a critical factor for tumor growth in human esophageal squamous cell carcinoma and its clinical significance.
  Int J Cancer, 122, 325-332.  
17881001 A.Mahajan, Y.Guo, C.Yuan, C.M.Weghorst, M.D.Tsai, and J.Li (2007).
Dissection of protein-protein interaction and CDK4 inhibition in the oncogenic versus tumor suppressing functions of gankyrin and P16.
  J Mol Biol, 373, 990.  
17174335 D.U.Ferreiro, C.F.Cervantes, S.M.Truhlar, S.S.Cho, P.G.Wolynes, and E.A.Komives (2007).
Stabilizing IkappaBalpha by "consensus" design.
  J Mol Biol, 365, 1201-1216.  
17292836 Y.Nakamura, K.Nakano, T.Umehara, M.Kimura, Y.Hayashizaki, A.Tanaka, M.Horikoshi, B.Padmanabhan, and S.Yokoyama (2007).
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome.
  Structure, 15, 179-189.
PDB codes: 2dvw 2dwz
  17329811 Y.Nakamura, T.Umehara, A.Tanaka, M.Horikoshi, B.Padmanabhan, and S.Yokoyama (2007).
Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 190-192.  
15889240 B.A.Niemeyer (2005).
Structure-function analysis of TRPV channels.
  Naunyn Schmiedebergs Arch Pharmacol, 371, 285-294.  
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