1j1v
From Proteopedia
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|PDB= 1j1v |SIZE=350|CAPTION= <scene name='initialview01'>1j1v</scene>, resolution 2.1Å | |PDB= 1j1v |SIZE=350|CAPTION= <scene name='initialview01'>1j1v</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= DnaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= DnaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1v OCA], [http://www.ebi.ac.uk/pdbsum/1j1v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j1v RCSB]</span> | ||
}} | }} | ||
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[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:27:44 2008'' |
Revision as of 18:27, 30 March 2008
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| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | DnaA (Escherichia coli) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of DnaA domainIV complexed with DnaAbox DNA
Overview
Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal structure of its DNA-binding domain (domain IV) complexed with a DnaA box at 2.1 A resolution. DnaA domain IV contains a helix-turn-helix motif for DNA binding. One helix and a loop of the helix- turn-helix motif are inserted into the major groove and 5 bp (3' two-thirds of the DnaA box sequence) are recognized through base-specific hydrogen bonds and van der Waals contacts with the C5-methyl groups of thymines. In the minor groove, Arg399, located in the loop adjacent to the motif, recognizes three more base pairs (5' one-third of the DnaA box sequence) by base-specific hydrogen bonds. DNA bending by approximately 28 degrees was also observed in the complex. These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin.
About this Structure
1J1V is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structural basis of replication origin recognition by the DnaA protein., Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S, Nucleic Acids Res. 2003 Apr 15;31(8):2077-86. PMID:12682358
Page seeded by OCA on Sun Mar 30 21:27:44 2008
Categories: Escherichia coli | Single protein | Fujikawa, N. | Katayama, T. | Kurumizaka, H. | Nureki, O. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Shirouzu, M. | Terada, T. | Yokoyama, S. | Protein-dna complex | Replication | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
