P53-DNA Recognition: Difference between revisions
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{{BAMBED | |||
|DATE=July 26, 2012 | |||
|OLDID=1472467 | |||
|BAMBEDDOI=10.1002/bmb.20650 | |||
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<StructureSection load='' size='400' side='right' ' oldscene='Sandbox_Reserved_170/Complex/6' scene='P53-DNA_Recognition/P53_complex/1' caption='Human p53 core complex with DNA (PDB code [[3kz8]]).'> | |||
''This is a joint project of students at La Cañada High School, La Cañada Flintridge, California USA, and students at the University of Southern California, Los Angeles, California USA, mentored by [[User:Remo Rohs|Professor Remo Rohs]].'' | ''This is a joint project of students at La Cañada High School, La Cañada Flintridge, California USA, and students at the University of Southern California, Los Angeles, California USA, mentored by [[User:Remo Rohs|Professor Remo Rohs]].'' | ||
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==Introduction and Biological Role of the Tumor Suppressor p53== | ==Introduction and Biological Role of the Tumor Suppressor p53== | ||
[[Image:p53-intro.jpg|thumb|left|300px|Figure 1: Crystal structure of a p53 DBD tetramer-DNA complex; [ | [[Image:p53-intro.jpg|thumb|left|300px|Figure 1: Crystal structure of a p53 DBD tetramer-DNA complex; [[3kz8|PDB ID# 3KZ8]]<ref name='kitayner'>Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol. 2010;17(4):423-9. [http://www.ncbi.nlm.nih.gov/pubmed/20364130 PMID:20364130].</ref>.]] | ||
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[[Image:consensus.jpg|thumb| | [[Image:consensus.jpg|thumb|left|250px|Figure 2: p53 consensus site; R= A or G, Y= C or T, and W=A or T.]] | ||
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[[Image:p53-domains.jpg|thumb| | [[Image:p53-domains.jpg|thumb|left|400px|Figure 3: Frequency of p53 mutants associated with cancer derived from [http://www-p53.iarc.fr/ IARC TP53 database]. Domain architecture; N-ter=N-terminal, DBD=DNA binding domain<ref name='kitayner'/>, Tet=Tetramerization<ref name='tetra'>Jeffrey PD, Gorina S, Pavletich NP. Crystal structure of the p53 tetramerization domain. Science 1995;267:1498-502. [http://www.ncbi.nlm.nih.gov/pubmed/7878469 PMID:7878469].</ref>, and C-ter=C-terminal domain. Intermediate regions are fairly disordered.]] | ||
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Also known as the '''Guardian of the Genome''', the tumor suppressor p53 is crucial in the natural defense against human cancer. The protein is activated by stress factors that can compromise the genomic integrity of the cell. This activation unleashes the function of p53 as a [[transcription factor]]. It binds as a tetramer ('''Figure 1''') to a large range of DNA response elements. The p53 consensus site ('''Figure 2''') is formed by two decameric half-sites, each containing a core element (red), that are separated by a variable number of base pairs (blue). | Also known as the '''Guardian of the Genome''', the tumor suppressor p53 is crucial in the natural defense against human cancer. The protein is activated by stress factors that can compromise the genomic integrity of the cell. This activation unleashes the function of p53 as a [[transcription factor]]. It binds as a tetramer ('''Figure 1''') to a large range of DNA response elements. The p53 consensus site ('''Figure 2''') is formed by two decameric half-sites, each containing a core element (red), that are separated by a variable number of base pairs (blue). | ||
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===Domain Architecture and Tetramerization=== | ===Domain Architecture and Tetramerization=== | ||
The p53 protein consists of the N-terminal transactivation domain, the DNA binding domain ('''DBD''') or core, the tetramerization domain ([[#Tetramerization Domain|see its structure below]]), and the C-terminal regulatory domain ('''Figure 3'''). This Proteopedia page discusses protein-DNA recognition by p53, thus focusing on the DBD of p53 (<scene oldname='Sandbox_Reserved_170/Complex/6' name='P53-DNA_Recognition/P53_complex/1'>Figure 4: Crystal structure of p53 DBD tetramer-DNA complex</scene>, [[3kz8|PDB ID 3KZ8]]). | |||
The p53 protein consists of the N-terminal transactivation domain, the DNA binding domain ('''DBD''') or core, the tetramerization domain, and the C-terminal regulatory domain ('''Figure 3'''). This Proteopedia page discusses protein-DNA recognition by p53, thus focusing on the DBD of p53 ( | |||
The DBD in tetrameric form binds to a <font color="#e06000">'''DNA response element'''</font> | The DBD in tetrameric form binds to a <font color="#e06000">'''DNA response element'''</font>, which consists of two DNA half sites. These decameric half sites can be separated by a DNA spacer of flexible length but in this case, the spacer is of length zero base pairs. The <scene oldname='Sandbox_Reserved_170/Complex/7' name='P53-DNA_Recognition/P53_complex/2'>p53 tetramer binds DNA as a dimer of dimers</scene> with each <font color='e000e0'>'''magenta'''</font>-<font color='00c0c0'>'''cyan'''</font> dimer binding to one half site of the response element<ref>Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z. Structural basis of DNA recognition by p53 tetramers. Mol Cell. 2006 Jun 23;22(6):741-53. [http://www.ncbi.nlm.nih.gov/pubmed/16793544 PMID:16793544].</ref>. | ||
The p53 DBD assumes the conformation of an <scene name='Sandbox_Reserved_170/Beta/1'>immunoglobulin-like fold consisting of a beta sandwich</scene>, which binds the response element in the major groove. A functionally important <scene name='Sandbox_Reserved_170/Zn/1'>Zn2+ ion coordinates the Cys176, His179, Cys238, Cys242 residues</scene> and, thus, stabilizes the fold of the DBD. | The p53 DBD assumes the conformation of an <scene name='Sandbox_Reserved_170/Beta/1'>immunoglobulin-like fold consisting of a beta sandwich</scene>, which binds the response element in the major groove. A functionally important <scene name='Sandbox_Reserved_170/Zn/1'>Zn2+ ion coordinates the Cys176, His179, Cys238, Cys242 residues</scene> and, thus, stabilizes the fold of the DBD. | ||
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===Protein-Protein Interactions=== | ===Protein-Protein Interactions=== | ||
The human p53 tetramer forms a relatively small <scene | The human p53 tetramer forms a relatively small <scene oldname='Sandbox_Reserved_170/Intra-dimer/4' name='P53-DNA_Recognition/P53_intra-dimer/2'>intra-dimer interface with two salt bridges between Glu180 and Arg181 residues</scene> and, in comparison, a large <scene name='Sandbox_Reserved_170/Inter-dimer/4'>inter-dimer interface with an extensive network of interactions</scene>. The actual molecular interactions and strength in binding can vary as functions of the sequence and spacer length of the response element. | ||
===Major Groove Base Readout=== | ===Major Groove Base Readout=== | ||
[[Image:p53-motif.jpg|thumb|right|300px|Figure | [[Image:p53-motif.jpg|thumb|right|300px|Figure 5: p53 binding site motif with G/C base pairs most conserved. PLoS has provided permission for usage of this figure<ref>Horvath MM, Wang X, Resnick MA, Bell DA. Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PLoS Genet. 2007 Jul;3(7):e127. [http://www.ncbi.nlm.nih.gov/pubmed/17677004 PMID:17677004].</ref>.]] | ||
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Protein side chains and base pairs form direct contacts in the major groove. Among which, the <scene name='Sandbox_Reserved_170/Arg280_contact/5'>contact between Arg280 and the guanine of the core element</scene> contributes most to binding specificity. This highly specific readout is due to the <scene | Protein side chains and base pairs form direct contacts in the major groove. Among which, the <scene name='Sandbox_Reserved_170/Arg280_contact/5'>contact between Arg280 and the guanine of the core element</scene> contributes most to binding specificity. This highly specific readout is due to the <scene oldname='Sandbox_Reserved_170/Arg280_contact/4' name='P53-DNA_Recognition/P53_arg280_contact/1'>bidentate hydrogen bond formed between Arg280 and guanine</scene>. As a result of this '''base readout''' the G/C base pairs in the CWWG core elements are the most conserved positions in p53 response elements ('''Figure 5'''). | ||
Another important contact is formed with the <scene name='Sandbox_Reserved_170/Lys_120/3'>Lys120 residue from the L1 loop of the protein</scene>. Lys120 is very important biologically because acetylation of this residue is known to trigger the apoptotic response of p53. | Another important contact is formed with the <scene name='Sandbox_Reserved_170/Lys_120/3'>Lys120 residue from the L1 loop of the protein</scene>. Lys120 is very important biologically because acetylation of this residue is known to trigger the apoptotic response of p53. | ||
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Another arginine residue, <scene name='Sandbox_Reserved_170/Arg273/2'>Arg273, contacts the phosphodiester backbone</scene> forming a salt bridge, and seems to be important for human p53-DNA binding. Moreover, Arg273 is the second most common missense mutation in human cancer ('''Figure 3'''). | Another arginine residue, <scene name='Sandbox_Reserved_170/Arg273/2'>Arg273, contacts the phosphodiester backbone</scene> forming a salt bridge, and seems to be important for human p53-DNA binding. Moreover, Arg273 is the second most common missense mutation in human cancer ('''Figure 3'''). | ||
[[Image:Kitayner-etal-Figure7.jpg|thumb|right|400px|Figure | [[Image:Kitayner-etal-Figure7.jpg|thumb|right|400px|Figure 6: DNA shape readout of narrow minor groove regions with enhanced electrostatic potential by Arg248. Nature Publishing Group has provided permission for usage of this figure<ref name='kitayner'/>.]] | ||
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===Minor Groove Shape Readout=== | ===Minor Groove Shape Readout=== | ||
Most commonly, however, the residue Arg248 is found mutated in human tumors. <scene name='Sandbox_Reserved_170/Arg248/2'>Arg248 contacts the minor groove</scene> although it does not usually form hydrogen bonds with the bases. Arg248 was shown to recognize regions of narrow minor groove associated with enhanced negative electrostatic potential ('''Figure | Most commonly, however, the residue Arg248 is found mutated in human tumors. <scene name='Sandbox_Reserved_170/Arg248/2'>Arg248 contacts the minor groove</scene> although it does not usually form hydrogen bonds with the bases. Arg248 was shown to recognize regions of narrow minor groove associated with enhanced negative electrostatic potential ('''Figure 6''')<ref name='kitayner'/>. This observation provides a novel molecular explanation of the importance of Arg248 for p53-DNA binding and its role in cancer. The described mechanism known as '''shape readout''' was found to be broadly employed by arginine residues<ref name="nature">Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461(7268):1248-53. [http://www.ncbi.nlm.nih.gov/pubmed/19865164 PMID:19865164].</ref>. | ||
==Hoogsteen vs. Watson-Crick Base Pair in p53 Binding Sites== | ==Hoogsteen vs. Watson-Crick Base Pair in p53 Binding Sites== | ||
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The reason for this deformation of the double helix is the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>base pairing geometry in Hoogsteen base pairs</scene> with the approximately 180 degree rotation of adenine around the glycosidic bond and formation of hydrogen bonds with thymine at a different edge of the adenine base compared to <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairing</scene>, depicted here for the identical base pair in a p53 response element with different sequence from [[3kmd|PDB ID# 3KMD]]. | The reason for this deformation of the double helix is the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>base pairing geometry in Hoogsteen base pairs</scene> with the approximately 180 degree rotation of adenine around the glycosidic bond and formation of hydrogen bonds with thymine at a different edge of the adenine base compared to <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairing</scene>, depicted here for the identical base pair in a p53 response element with different sequence from [[3kmd|PDB ID# 3KMD]]. | ||
==Tetramerization Domain== | |||
Aside from the DBD, the only other domain for which structural information is available is the ''tetramerization domain'' [<scene name='Sandbox_Reserved_170/Tetra/2'>Figure 7: Crystal structure of p53 tetramerization domain</scene>, ([[1c26|PDB ID 1C26]])], which forms as a dimer of dimers with one alpha helix and one beta strand contributed by each p53 monomer. The tetramerization domain is ''not present'' in the crystal structure of the DBD (<scene oldname='Sandbox_Reserved_170/Complex/6' name='P53-DNA_Recognition/P53_complex/1'>Figure 4: Crystal structure of p53 DBD tetramer-DNA complex</scene>). | |||
=Further Reading= | =Further Reading= | ||
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A more general discussion of structural origins of binding specificity in protein-DNA recognition has been published along with a suggestion for a new '''classification of protein-DNA readout modes''' that goes beyond the historical description of direct and indirect readout<ref name="annualreview">Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 2010;79:233-69. [http://www.ncbi.nlm.nih.gov/pubmed/20334529 PMID:20334529].</ref>.<br/> | A more general discussion of structural origins of binding specificity in protein-DNA recognition has been published along with a suggestion for a new '''classification of protein-DNA readout modes''' that goes beyond the historical description of direct and indirect readout<ref name="annualreview">Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 2010;79:233-69. [http://www.ncbi.nlm.nih.gov/pubmed/20334529 PMID:20334529].</ref>.<br/> | ||
</StructureSection> | |||
=3D structures of p53= | |||
[[P53]] | |||
=Acknowledgements= | =Acknowledgements= | ||
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=References= | =References= | ||
<references/> | <references/> | ||
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