Mid-Term Examination 11/14/00

 Part I

Tumor protein p53, a nuclear protein, plays an essential role in the regulation of cell cycle, specifically in the transition from G0 to G1. It is found in very low levels in normal cells, however, in a variety of transformed cell lines, it is expressed in high amounts, and believed to contribute to transformation and malignancy. p53 is a DNA- binding protein containing DNA-binding,oligomerization and transcription activation domains. It is postulated to bind as a tetramer to a p53-binding site and activate expression of downstream genes that inhibit growth and/or invasion, and thus function as a tumor suppressor. Mutants of p53 that frequently occur in a number of different human cancers fail to bind the consensus DNA binding site, and hence cause the loss of tumor suppressor activity. Alterations of the TP53 gene occur not only as somatic mutations in human malignancies, but also as germline mutations in some cancer-prone families with Li-Fraumeni syndrome.

a) What is the cytogenetic position of p53 in the CytogeneticMap?

 Ans:17p13.1

b) Which chromosome is this gene located ?

 Ans:17

c) What is its LocusID ?

 Ans:7157

d) What is the percent identity between H. sapiens, M. musculus and R. norvegicus of Tp53 ?

 Ans: H.sapiens     100 % / 392 aa
      M.musculus    77 % / 395 aa
      R.norvegicus  77 % / 392 aa

e) Find a paper that identified p53 as a sequence-specific DNA-binding protein. The authors are in the department of pathology, Johns Hopkins University of Medicine. Give the name of Journal, Vol. #, page # and year.

  Ans: Science 1991 Jun 21;252(5013):1708-11

f) Show the protein sequence of p53. (in fasta format)

 Ans: 
>gi|8400738|ref|NP_000537.2| tumor protein p53 [Homo sapiens]
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGR
DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

g) Find the PDB ID of crystal structure of p53 tetramerization domain and core domain with DNA.

 Ans:p53 tetramerization domain:1AIE
     p53 core domain:1TSR

 Part II 

Structural Bioinformatics part

Problems:

(1) Here is a serine protease protein, whose catalytic residues are Asp, His and Ser, respectively, known as the "catalytic triad". These residues are interacting with each other through hydrogen bonds. Please find the possible catalytic triads of this protein.

  Ans:Asp36 Ser38 His39

(2) Find the possible DNA binding site of the protein, a subunit of the tumor suppressor P53. (Hint: use sPDBview to draw the molecular surface)

 Ans:
 

   red:helix  blue:sheet
   DNA binding sites are most helix-turn-helix motif.There are three helices
   in above picture and the right hand helix is at the end.So other two helices
   and mid white sequence (turn) may be the DNA binding site.


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