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1nzp

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{{STRUCTURE_1nzp| PDB=1nzp | SCENE= }}
{{STRUCTURE_1nzp| PDB=1nzp | SCENE= }}
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'''Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda'''
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===Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda===
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==Overview==
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DNA polymerase lambda (pol lambda) is a recently discovered nuclear enzyme belonging to the pol X family of DNA polymerases that exhibits a 32% sequence identity with the nuclear DNA repair protein, pol beta. Structural modeling suggests that pol lambda contains the palm, fingers, thumb, and 8 kDa lyase domains present in pol beta, as well as an additional N-terminal BRCT domain and a serine-proline-rich linker that are presumably involved in protein-protein interactions. The 8 kDa domain of pol beta is important for DNA binding and contains the dRP lyase activity, which is the rate-limiting step in the single-nucleotide base excision repair (BER) pathway of damaged DNA. Recently, it was shown that the 8 kDa domain of pol lambda also contains the dRP lyase activity. To gain further insight into the catalytic mechanism of dRP removal by pol lambda, we have determined the solution structure of the 8 kDa lyase domain of human DNA pol lambda via multidimensional NMR methods and the ARIA program. The resulting structures exhibited a high degree of similarity with the 8 kDa lyase domain of pol beta. Specifically, the side chains of residues W274, R275, Y279, K307, R308, and K312 are in similar positions to the functionally important side chains of residues H34, K35, Y39, K60, K68, and K72 in the 8 kDa lyase domain of pol beta. This suggests that, on the basis of the proposed roles of these residues in pol beta, the corresponding pol lambda side chains may be involved in DNA binding and dRP lyase activity. The structural alignment of W274 (pol lambda) with H34 (pol beta) indicates that the former is probably involved in a similar base stacking interaction with template DNA at the position of the gap, in contrast with several previous proposals which aligned D272 with H34. In a few cases for which there is a nonconservative substitution in the sequence alignment, a structural comparison shows a positionally and, hence, probably a functionally equivalent residue, e.g., K60 in pol beta and K307 in pol lambda. Additionally, on the basis of the structural alignment obtained, several previously proposed mechanistic hypotheses can be evaluated.
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{{ABSTRACT_PUBMED_12911298}}
==About this Structure==
==About this Structure==
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1NZP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZP OCA].
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1NZP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZP OCA].
==Reference==
==Reference==
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[[Category: Pol beta-like]]
[[Category: Pol beta-like]]
[[Category: Pol lambda]]
[[Category: Pol lambda]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:11:04 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:33:55 2008''

Revision as of 08:33, 29 July 2008

Image:1nzp.png

Template:STRUCTURE 1nzp

Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda

Template:ABSTRACT PUBMED 12911298

About this Structure

1NZP is a Single protein structure of sequence from Homo sapiens. Full experimental information is available from OCA.

Reference

Solution structure of the lyase domain of human DNA polymerase lambda., DeRose EF, Kirby TW, Mueller GA, Bebenek K, Garcia-Diaz M, Blanco L, Kunkel TA, London RE, Biochemistry. 2003 Aug 19;42(32):9564-74. PMID:12911298

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