5x4k: Difference between revisions

Latest revision as of 07:53, 22 November 2023

The complex crystal structure of Pyrococcus furiosus RecJ and CMP

Structural highlights

5x4k is a 1 chain structure with sequence from Pyrococcus furiosus DSM 3638. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.749Å
Ligands:	C5P, MSE, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8TZE0_PYRFU

Publication Abstract from PubMed

RecJ nucleases specifically degrade single-stranded (ss) DNA in the 5' to 3' direction. Archaeal RecJ is different from bacterial RecJ in sequence, domain organization, and substrate specificity. The RecJ from archaea Pyrococcus furiosus (PfuRecJ) also hydrolyzes RNA strands in the 3' to 5' direction. Like eukaryotic Cdc45 protein, archaeal RecJ forms a complex with MCM helicase and GINS. Here, we report the crystal structures of PfuRecJ and the complex of PfuRecJ and two CMPs. PfuRecJ bind one or two divalent metal ions in its crystal structure. A channel consisting of several positively charged residues is identified in the complex structure, and might be responsible for binding substrate ssDNA and/or releasing single nucleotide products. The deletion of the complex interaction domain (CID) increases the values of kcat/Km of 5' exonuclease activity on ssDNA and 3' exonuclease activity on ssRNA by 5- and 4-fold, respectively, indicating that the CID functions as a regulator of enzymatic activity. The DHH domain of PfuRecJ interacts with the C-terminal beta-sheet domain of the GINS51 subunit in the tetrameric GINS complex. The relationship of archaeal and bacterial RecJs, as well as eukaryotic Cdc45, is discussed based on biochemical and structural results.

The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45.,Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP Nucleic Acids Res. 2017 Dec 1;45(21):12551-12564. doi: 10.1093/nar/gkx887. PMID:30053256^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP. The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Nucleic Acids Res. 2017 Dec 1;45(21):12551-12564. doi: 10.1093/nar/gkx887. PMID:30053256 doi:https://dx.doi.org/10.1093/nar/gkx887

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OCA

[1] Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP. The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Nucleic Acids Res. 2017 Dec 1;45(21):12551-12564. doi: 10.1093/nar/gkx887. PMID:30053256 doi:https://dx.doi.org/10.1093/nar/gkx887

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5x4k' size='340' side='right'caption='[[5x4k]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5x4k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5x4k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X4K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.749&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x4h|5x4h]], [[5x4i|5x4i]], [[5x4j|5x4j]]</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=5x4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4k OCA], [https://pdbe.org/5x4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x4k RCSB], [https://www.ebi.ac.uk/pdbsum/5x4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4k ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF2055 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=5x4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4k OCA], [http://pdbe.org/5x4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4k RCSB], [http://www.ebi.ac.uk/pdbsum/5x4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4k ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8TZE0_PYRFU Q8TZE0_PYRFU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrfu]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Chen, J N]]
+[[Category: Chen JN]]
-[[Category: He, J H]]
+[[Category: He JH]]
-[[Category: Li, M J]]
+[[Category: Li MJ]]
-[[Category: Liu, X P]]
+[[Category: Liu XP]]
-[[Category: Wang, F P]]
+[[Category: Wang FP]]
-[[Category: Xiao, X]]
+[[Category: Xiao X]]
-[[Category: Xu, C Y]]
+[[Category: Xu CY]]
-[[Category: Yi, G S]]
+[[Category: Yi GS]]
-[[Category: Yu, F]]
+[[Category: Yu F]]
-[[Category: Zhou, H]]
+[[Category: Zhou H]]
-[[Category: Archaeal recj]]
-[[Category: Cmg interaction domain]]
-[[Category: Gin]]
-[[Category: Hydrolase]]
-[[Category: Interaction]]
-[[Category: Nuclease activity]]

5x4k: Difference between revisions

Latest revision as of 07:53, 22 November 2023

The complex crystal structure of Pyrococcus furiosus RecJ and CMP

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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