4beb

From Proteopedia

(Difference between revisions)

Current revision

MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

Structural highlights

4beb is a 4 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 2y3t. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.989Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T1R1_ECOLX The restriction (R) subunit of a type I restriction enzyme that recognizes 5'-GAAN(7)RTCG-3' and cleaves a random distance away. Subunit R is required for both nuclease and ATPase activities, but not for modification (Probable) (PubMed:12654995). After locating an unmethylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage (Probable). The enzyme undergoes major structural changes to bring the motor domains into contact with DNA, allowing DNA translocation. This prevents DNA access to the catalytic domains of both the R and M subunits, preventing both restriction and methylation (PubMed:32483229).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.

Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme.,Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R PLoS One. 2015 Jun 3;10(6):e0128700. doi: 10.1371/journal.pone.0128700., eCollection 2015. PMID:26039067^[5]

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

References

↑ Gao Y, Cao D, Zhu J, Feng H, Luo X, Liu S, Yan XX, Zhang X, Gao P. Structural insights into assembly, operation and inhibition of a type I restriction-modification system. Nat Microbiol. 2020 Jun 1. pii: 10.1038/s41564-020-0731-z. doi:, 10.1038/s41564-020-0731-z. PMID:32483229 doi:http://dx.doi.org/10.1038/s41564-020-0731-z
↑ Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 2003 Apr 1;31(7):1805-12. PMID:12654995
↑ Price C, Lingner J, Bickle TA, Firman K, Glover SW. Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. J Mol Biol. 1989 Jan 5;205(1):115-25. PMID:2784505 doi:10.1016/0022-2836(89)90369-0
↑ Gao Y, Cao D, Zhu J, Feng H, Luo X, Liu S, Yan XX, Zhang X, Gao P. Structural insights into assembly, operation and inhibition of a type I restriction-modification system. Nat Microbiol. 2020 Jun 1. pii: 10.1038/s41564-020-0731-z. doi:, 10.1038/s41564-020-0731-z. PMID:32483229 doi:http://dx.doi.org/10.1038/s41564-020-0731-z
↑ Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R. Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One. 2015 Jun 3;10(6):e0128700. doi: 10.1371/journal.pone.0128700., eCollection 2015. PMID:26039067 doi:http://dx.doi.org/10.1371/journal.pone.0128700

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4beb"

@@ Line 1: / Line 1: @@
 ==MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP==
-<StructureSection load='4beb' size='340' side='right' caption='[[4beb]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
+<StructureSection load='4beb' size='340' side='right'caption='[[4beb]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4beb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2y3t 2y3t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BEB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BEB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4beb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2y3t 2y3t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BEB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.989&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4be7|4be7]], [[4bec|4bec]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_I_site-specific_deoxyribonuclease Type I site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.3 3.1.21.3] </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=4beb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4beb OCA], [https://pdbe.org/4beb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4beb RCSB], [https://www.ebi.ac.uk/pdbsum/4beb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4beb ProSAT]</span></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=4beb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4beb OCA], [http://pdbe.org/4beb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4beb RCSB], [http://www.ebi.ac.uk/pdbsum/4beb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4beb ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/T1R1_ECOLX T1R1_ECOLX] The restriction (R) subunit of a type I restriction enzyme that recognizes 5'-GAAN(7)RTCG-3' and cleaves a random distance away. Subunit R is required for both nuclease and ATPase activities, but not for modification (Probable) (PubMed:12654995). After locating an unmethylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage (Probable). The enzyme undergoes major structural changes to bring the motor domains into contact with DNA, allowing DNA translocation. This prevents DNA access to the catalytic domains of both the R and M subunits, preventing both restriction and methylation (PubMed:32483229).<ref>PMID:32483229</ref> <ref>PMID:12654995</ref> <ref>PMID:2784505</ref> <ref>PMID:32483229</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Type I site-specific deoxyribonuclease]]
+[[Category: Large Structures]]
-[[Category: Baikova, T]]
+[[Category: Baikova T]]
-[[Category: Carey, J]]
+[[Category: Carey J]]
-[[Category: Csefalvay, E]]
+[[Category: Csefalvay E]]
-[[Category: Csefalvay, L]]
+[[Category: Csefalvay L]]
-[[Category: Ettrich, R]]
+[[Category: Ettrich R]]
-[[Category: Guzanova, A]]
+[[Category: Guzanova A]]
-[[Category: Janscak, P]]
+[[Category: Janscak P]]
-[[Category: Lapkouski, M]]
+[[Category: Lapkouski M]]
-[[Category: Panjikar, S]]
+[[Category: Panjikar S]]
-[[Category: Shevelev, I]]
+[[Category: Shevelev I]]
-[[Category: Smatanova, I K]]
+[[Category: Smatanova IK]]
-[[Category: Weiserova, M]]
+[[Category: Weiserova M]]
-[[Category: Dna modification]]
-[[Category: Hydrolase]]

4beb

From Proteopedia

Current revision

MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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