5j3n

From Proteopedia

(Difference between revisions)

Revision as of 10:44, 6 September 2023

C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin

Structural highlights

5j3n is a 2 chain structure with sequence from Aequorea victoria and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.45Å
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] GFP_AEQVI Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.

Publication Abstract from PubMed

Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 A, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique alpha-helical fold. The full-length HsdR model, based on the wild-type structure and the herein determined C-terminal domain, disclosed a proposed DNA-binding groove lined by positively charged residues. In vivo and in vitro assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, C-terminal domain revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.

Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.,Grinkevich P, Sinha D, Iermak I, Guzanova A, Weiserova M, Ludwig J, Mesters JR, Ettrich RH J Biol Chem. 2018 Jul 27. pii: RA118.003978. doi: 10.1074/jbc.RA118.003978. PMID:30054276^[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
↑ Grinkevich P, Sinha D, Iermak I, Guzanova A, Weiserova M, Ludwig J, Mesters JR, Ettrich RH. Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding. J Biol Chem. 2018 Jul 27. pii: RA118.003978. doi: 10.1074/jbc.RA118.003978. PMID:30054276 doi:http://dx.doi.org/10.1074/jbc.RA118.003978

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5j3n"

@@ Line 1: / Line 1: @@
 ==C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin==
-<StructureSection load='5j3n' size='340' side='right' caption='[[5j3n]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+<StructureSection load='5j3n' size='340' side='right'caption='[[5j3n]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3N FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</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]] 2.45&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hsdR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [http://pdbe.org/5j3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [http://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n 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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [https://pdbe.org/5j3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [https://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
+[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> [https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 ==See Also==
-*[[Green Fluorescent Protein|Green Fluorescent Protein]]
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Aequorea victoria]]
-[[Category: Ettrich, R]]
+[[Category: Escherichia coli]]
-[[Category: Grinkevich, P]]
+[[Category: Large Structures]]
-[[Category: Iermak, I]]
+[[Category: Ettrich R]]
-[[Category: Ludwig, J]]
+[[Category: Grinkevich P]]
-[[Category: Luedtke, N]]
+[[Category: Iermak I]]
-[[Category: Mesters, J R]]
+[[Category: Ludwig J]]
-[[Category: Ecor124i]]
+[[Category: Luedtke N]]
-[[Category: Fusion protein]]
+[[Category: Mesters JR]]
-[[Category: Gfp]]
-[[Category: Hsdr]]
-[[Category: Hydrolase]]
-[[Category: Phluorin]]
-[[Category: Type i restriction-modification system]]

5j3n

From Proteopedia

Revision as of 10:44, 6 September 2023

C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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