Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (413K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (9)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Swalla, B. M.
Right arrow Articles by Gardner, J. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Swalla, B. M.
Right arrow Articles by Gardner, J. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 3 805-818
© 2003 Oxford University Press

Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain

Brian M. Swalla*, Richard I. Gumport1 and Jeffrey F. Gardner2

Optigenix Inc., Lewisville, PA 19351, USA, 1 Department of Biochemistry and College of Medicine and 2 Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

*To whom correspondence should be addressed. Tel: +1 217 333 7287; Fax: +1 217 244 6697; Email: b-swalla{at}life.uiuc.edu

Tyrosine recombinases participate in diverse biological processes by catalyzing recombination between specific DNA sites. Although a conserved protein fold has been described for the catalytic (CAT) domains of five recombinases, structural relationships between their core-binding (CB) domains remain unclear. Despite differences in the specificity and affinity of core-type DNA recognition, a conserved binding mechanism is suggested by the shared two-domain motif in crystal structure models of the recombinases Cre, XerD and Flp. We have found additional evidence for conservation of the CB domain fold. Comparison of XerD and Cre crystal structures showed that their CB domains are closely related; the three central {alpha}-helices of these domains are superposable to within 1.44 Å. A structure-based multiple sequence alignment containing 25 diverse CB domain sequences provided evidence for widespread conservation of both structural and functional elements in this fold. Based upon the Cre and XerD crystal structures, we employed homology modeling to construct a three-dimensional structure for the {lambda} integrase CB domain. The model provides a conceptual framework within which many previously identified, functionally important amino acid residues were investigated. In addition, the model predicts new residues that may participate in core-type DNA binding or dimerization, thereby providing hypotheses for future genetic and biochemical experiments.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
G. Dhar, M. M. McLean, J. K. Heiss, and R. C. Johnson
The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands
Nucleic Acids Res., August 1, 2009; 37(14): 4743 - 4756.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Malanowska, J. Cioni, B. M. Swalla, A. Salyers, and J. F. Gardner
Mutational Analysis and Homology-Based Modeling of the IntDOT Core-Binding Domain
J. Bacteriol., April 1, 2009; 191(7): 2330 - 2339.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. Flanigan and J. F. Gardner
Interaction of the Gifsy-1 Xis Protein with the Gifsy-1 attP Sequence
J. Bacteriol., September 1, 2007; 189(17): 6303 - 6311.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
G. Panis, V. Mejean, and M. Ansaldi
Control and Regulation of KplE1 Prophage Site-specific Recombination: A NEW RECOMBINATION MODULE ANALYZED
J. Biol. Chem., July 27, 2007; 282(30): 21798 - 21809.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Sauer and J. McDermott
DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages
Nucleic Acids Res., November 18, 2004; 32(20): 6086 - 6095.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.