2w00

Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP

Structural highlights

2w00 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	ATP, MG, MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T1R1_ECOLX The restriction (R) subunit of a type I restriction enzyme that recognizes 5'-GAAN(6)RTCG-3' (for EcoR124I) and 5'-GAAN(7)RTCG-3' (for EcoR124II) and cleaves a random distance away (PubMed:2784505). 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 (PubMed:15300241). 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). The R(1)M(2)S(1) complex translocates an average of 555 bp/second on nicked DNA; the R(2)M(2)S(1) complex translocates at double that speed (PubMed:15300241). The 2 R subunit motors are independent and track along the helical pitch of the DNA, inducing positive supercoiling ahead of themselves (PubMed:15300241).^[1] ^[2] ^[3] ^[4] ^[5]

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

Type I restriction-modification enzymes act as conventional adenine methylases on hemimethylated DNAs, but unmethylated recognition targets induce them to translocate thousands of base pairs before cleaving distant sites nonspecifically. The first crystal structure of a type I motor subunit responsible for translocation and cleavage suggests how the pentameric translocating complex is assembled and provides a structural framework for translocation of duplex DNA by RecA-like ATPase motors.

Structure of the motor subunit of type I restriction-modification complex EcoR124I.,Lapkouski M, Panjikar S, Janscak P, Smatanova IK, Carey J, Ettrich R, Csefalvay E Nat Struct Mol Biol. 2008 Dec 14. PMID:19079266^[6]

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

References

↑ Seidel R, van Noort J, van der Scheer C, Bloom JG, Dekker NH, Dutta CF, Blundell A, Robinson T, Firman K, Dekker C. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat Struct Mol Biol. 2004 Sep;11(9):838-43. PMID:15300241 doi:10.1038/nsmb816
↑ 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:https://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
↑ 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:https://dx.doi.org/10.1038/s41564-020-0731-z
↑ Lapkouski M, Panjikar S, Janscak P, Smatanova IK, Carey J, Ettrich R, Csefalvay E. Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat Struct Mol Biol. 2008 Dec 14. PMID:19079266 doi:nsmb.1523

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Seidel R, van Noort J, van der Scheer C, Bloom JG, Dekker NH, Dutta CF, Blundell A, Robinson T, Firman K, Dekker C. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat Struct Mol Biol. 2004 Sep;11(9):838-43. PMID:15300241 doi:10.1038/nsmb816

[2] 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

[3] 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:https://dx.doi.org/10.1038/s41564-020-0731-z

[4] 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

[5] 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:https://dx.doi.org/10.1038/s41564-020-0731-z

[6] Lapkouski M, Panjikar S, Janscak P, Smatanova IK, Carey J, Ettrich R, Csefalvay E. Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat Struct Mol Biol. 2008 Dec 14. PMID:19079266 doi:nsmb.1523

[1]

[2]

[3]

[4]

[5]

[6]

2w00

Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools