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| | ==Neisseria gonorrhoeae PriB== | | ==Neisseria gonorrhoeae PriB== |
| - | <StructureSection load='3k8a' size='340' side='right' caption='[[3k8a]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='3k8a' size='340' side='right'caption='[[3k8a]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3k8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neig1 Neig1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K8A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3k8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae_FA_1090 Neisseria gonorrhoeae FA 1090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K8A FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NGO0582, prib ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242231 NEIG1])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3k8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k8a OCA], [http://pdbe.org/3k8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k8a RCSB], [http://www.ebi.ac.uk/pdbsum/3k8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k8a ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k8a OCA], [https://pdbe.org/3k8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k8a RCSB], [https://www.ebi.ac.uk/pdbsum/3k8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k8a ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PRIB_NEIG1 PRIB_NEIG1] Stimulates the DNA unwinding activity of PriA helicase, which does not seem to require single-stranded DNA-binding by PriB. Activates DNA-dependent ATP hydrolysis catalyzed by PriA (PubMed:21861872). Has a weak single-stranded DNA-binding activity (PubMed:21861872, PubMed:19906704). Binds weakly also double-stranded DNA, a partial duplex DNA with a 3' single-stranded DNA overhang, and a forked DNA structure with fully duplex leading and lagging strand arms in vitro (PubMed:21861872).<ref>PMID:19906704</ref> <ref>PMID:21861872</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/3k8a_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/3k8a_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Neig1]] | + | [[Category: Large Structures]] |
| - | [[Category: DeBeer, M A]] | + | [[Category: Neisseria gonorrhoeae FA 1090]] |
| - | [[Category: Dong, J]] | + | [[Category: DeBeer MA]] |
| - | [[Category: Duckett, K L]] | + | [[Category: Dong J]] |
| - | [[Category: George, N P]] | + | [[Category: Duckett KL]] |
| - | [[Category: Lopper, M E]] | + | [[Category: George NP]] |
| - | [[Category: Beta-barrel]] | + | [[Category: Lopper ME]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Ob-fold]]
| + | |
| Structural highlights
Function
PRIB_NEIG1 Stimulates the DNA unwinding activity of PriA helicase, which does not seem to require single-stranded DNA-binding by PriB. Activates DNA-dependent ATP hydrolysis catalyzed by PriA (PubMed:21861872). Has a weak single-stranded DNA-binding activity (PubMed:21861872, PubMed:19906704). Binds weakly also double-stranded DNA, a partial duplex DNA with a 3' single-stranded DNA overhang, and a forked DNA structure with fully duplex leading and lagging strand arms in vitro (PubMed:21861872).[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Reactivation of repaired DNA replication forks is essential for complete duplication of bacterial genomes. However, not all bacteria encode homologs of the well-studied Escherichia coli DNA replication restart primosome proteins, suggesting that there might be distinct mechanistic differences among DNA replication restart pathways in diverse bacteria. Since reactivation of repaired DNA replication forks requires coordinated DNA and protein binding by DNA replication restart primosome proteins, we determined the crystal structure of Neisseria gonorrhoeae PriB at 2.7 A resolution and investigated its ability to physically interact with DNA and PriA helicase. Comparison of the crystal structures of PriB from N. gonorrhoeae and E. coli reveals a well-conserved homodimeric structure consisting of two oligosaccharide/oligonucleotide-binding (OB) folds. In spite of their overall structural similarity, there is significant species variation in the type and distribution of surface amino acid residues. This correlates with striking differences in the affinity with which each PriB homolog binds single-stranded DNA and PriA helicase. These results provide evidence that mechanisms of DNA replication restart are not identical across diverse species and that these pathways have likely become specialized to meet the needs of individual organisms.
The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways.,Dong J, George NP, Duckett KL, DeBeer MA, Lopper ME Nucleic Acids Res. 2010 Jan;38(2):499-509. Epub 2009 Nov 11. PMID:19906704[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dong J, George NP, Duckett KL, DeBeer MA, Lopper ME. The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways. Nucleic Acids Res. 2010 Jan;38(2):499-509. Epub 2009 Nov 11. PMID:19906704 doi:10.1093/nar/gkp1031
- ↑ Feng C, Sunchu B, Greenwood ME, Lopper ME. A bacterial PriB with weak single-stranded DNA binding activity can stimulate the DNA unwinding activity of its cognate PriA helicase. BMC Microbiol. 2011 Aug 23;11:189. PMID:21861872 doi:10.1186/1471-2180-11-189
- ↑ Dong J, George NP, Duckett KL, DeBeer MA, Lopper ME. The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways. Nucleic Acids Res. 2010 Jan;38(2):499-509. Epub 2009 Nov 11. PMID:19906704 doi:10.1093/nar/gkp1031
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