Ribonuclease

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Template:STRUCTURE 1jvt

Ribonuclease (RNase) degrades RNA. The endonucleases cleave single or double stranded RNA and include RNase III, A, T1 H and P. Exo-RNases remove terminal nucleotide
from the ends of the RNA molecule. They include RNase II D, T, PH, Polynucleotide Phosphorylase (PNPase) and oligoribonuclease (ORNase).
 RNase A cleaves C or U of single-stranded RNA (ssRNA). RNase BA is RNase from Bacillus amyloliquefaciens. RNase D degrades 3'-end pre-tRNA. RNase H cleaves RNA/DNA double-strand to produce ssDNA. RNase I cleaves 3'-end of ssRNA. RNase II degrades 3'-end ssRNA. RNase III cleaves rRNA. RNase P is a ribozyme. RNase S is RNase A cleaved by subtilisin. RNase SA is RNase from Streptomyces auerofaciens. RNase T is involved in RNA maturation. RNase T1 cleaves 3'-end G from ssRNA. RNase U2 cleaves 3'-end A from ssRNA.

3D Structures of Ribonuclease

RNase I

3mwq, 3mwq, 3mx8, 3i67, 3i6f, 3i6h, 3i6j, 3i7w, 3eux, 3euy, 3euz, 3ev0, 3ev1, 3ev2, 3ev3, 3ev4, 3ev5, 3ev6, 3dh5, 2e3w, 2g4w, 2g4x, 2gbq, 2blp, 2blz, 1jvt, 1jvv, 1js0, 1fs3, 1kf2, 1kf3, 1kf4, 1kf5, 1kf7, 1kf8, 1aqp, 1a2w, 1rnw, 1rnz, 1rno, 1rnq, 1rbx, 1ssc, 3srn, 4srn, 1srn, 5rsa - bRNase I pancreatic - bovine

3a1r - bRNase I pancreatic - neutron

3i7x, 3i7y, 3fkz, 3fl3, 3dh6, 3di7, 3di8, 3di9, 3dib, 3dic, 2oqf, 3bcm, 3bco, 3bcp, 2nui, 2op2, 1ymn, 1ymr, 1ymw, 2apq, 1izp, 1izq, 1izr, 1kh8, 1c8w, 1eic, 1eid, 1eie, 1dy5, 3rsd, 3rsk, 1ssa, 1ssb - bRNase I pancreatic (mutant)

3lxo, 3jw1, 3djo, 3djp, 3djq, 3djv, 3djx, 3dxg, 3dxh, 2w5g, 2w5i, 2w5k, 2w5l, 2w5m, 3d6o, 3d6p, 3d6q, 3d7b, 3d8y, 3d8z, 2qca, 2g8r, 1z6d, 1z6s, 1u1b, 1w4o, 1w4p, 1w4q, 1wbu, 1o0f, 1jn4, 1jvu, 1f0v, 1ruv, 1rnm, 1rnn, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rnc, 1rnd, 1rob, 1rta, 1rtb - bRNase I pancreatic + nucleotide

6rsa - bRNase I pancreatic + nucleotide - neutron

3fl0, 3fl1, 4rsk - bRNase I pancreatic (mutant) + nucleotide

 2xog, 2xoi, 2q4g, 1dfj - bRNase I pancreatic + inhibitor

1rar, 1ras - bRNase I pancreatic fluorescent
 2p42, 2p43, 2p44, 2p45 , 2p46, 2p47, 2p48, 2p49, 2p4a, 1bzq - bRNase I + antibody

3f8g, 2e0j, 2e0l, 2e0m, 2e0o, 1h8x, 1e21, 1dza - hRNase I pancreatic (mutant) - human

2k11 - hRNase I pancreatic]] - NMR

 1z7x - hRNase I + inhibitor

3ljd, 3ln8, 2vq8, 2vq9 - ZeRNase I – Zebrafish

2pqx, 2pqy - EcRNase I
 - Escherichia coli
2z70, 2ea1 - EcRNAse I + DNA





 RNase II

2ix0, 2id0 - EcRNase II

2ix1 - EcRNase II (mutant)

1m58, 1km8, 1km9- BuRNase 2 - Bullfrog
 1bc4 - BuRNase 2 - NMR

 1m07 - BuRNase 2 + DNA




RNase III

2nue, 2nuf, 2nug, 1yyk, 1yyw - AaRNase III + RNA - Aquifex aeolicus
2ez6, 1yyo, 1yz9, 1rc7 - AaRNase III (mutant) + RNA 

1rc5, 1i4s, 1jfz - AaRNase III N-terminal

1z5f - BuRNase III
2a11 - MtRNase III - Mycobacterium tuberculosis
1o0w - TmRNase III - Thermotoga maritima

 2kb5 - hRNase 3 - NMR

 1dyt, 1qmt - hRNase 3

1h1h - hRNase 3 + nucleotide




RNase 4

1wdy - hRNase 4

2rnf, 1rnf - hRNase 4 + nucleotide

 1kvz - BuRNase 4 - NMR




RNase 5

1un3, 1un4, 1un5, 1gv7 - hRNase 5 (mutant)

1h0d - hRNase 5 + antibody

3lje - ZeRNase 5

RNase 7



2hky - hRNase 7 - NMR




RNase A

1rra - RNase A (mutant) – rat

RNase BA

1x1u, 1x1x, 1x1y, 1b27, 1b2u, 1b3s - BaRNase BA + Barstar (mutant) - Bacillus amyloliquefaciens

3da7, 1brs, 1bgs - BaRNase BA + Barstar

 1b2s, 2za4 - BaRNase BA (mutant) + Barstar (mutant)
1brn, 2kf5, 2kf6, 1rnb - BaRNase BA + nucleotide

3kch, 2f4y, 2f56, 2f5m, 2f5w - BaRNase BA crosslinked

2kf3, 2kf4, 1fw7, 1bnr - BaRNase BA – NMR

1yvs, 1b2x, 1a2p, 1bni, 1bnj - BaRNase BA 

1b20, 1b21, 1b2z, 1bne, 1bnf, 1bng, 1brh, 1bri, 1brj, 1brk, 1bns, 1brg, 1bsa, 1bsb, 1bsc, 1bsd, 1bse, 1ban, 1bao - BaRNase BA (mutant)



RNase D

1yt3 - EcRNase D



RNase E

2vmk, 2c4r, 2bx2 - EcRNase E catalytic domain

1slj - EcRNase E S1 domain - NMR

 1smx, 1sn8 - EcRNase E S1 domain 

2vrt, 2c0b - EcRNase E catalytic domain + RNA

RNase H

3h7i, 3h8s, 3h8w - T4RNase H (mutant) - Enterobacteria phage T4

2ihn - T4RNase H (mutant) + DNA

 3h8j, 1tfr- T4RNase H

 2rpi, 1ril - TtRNase H - Thermus thermophilus - NMR

 1jl2 - EcRNase H /TtRNase H

 3d0p - BhRNase H (mutant) + DNA - Bacillus halodurans

1zbf - BhRNase H (mutant)

 2r7y, 2g8f, 2g8h, 2g8i, 2g8k, 2g8u, 2g8v, 2g8w, 1zbi, 1zbl - BhRNase H (mutant) + RNA + DNA




RNase HI

2qk9, 2qkb, 2qkk - hRNase HI (mutant) + RNA + DNA

 3h08 - RNase HI - Chlorobaculum tepidum
3aa2, 3aa3, 3aa4, 3aa5, 2yv0, 2z1g, 2z1h, 2z1i, 2z1j, 1wse, 1wsf, 1wsg, 1wsh, 1wsi, 1wsj, 1jxb, 1jl1, 1f21, 1kva, 1kvb, 1kvc, 1goa, 1gob, 1goc - EcRNase HI (mutant)

 1g15, 1rdd - EcRNase HI

1rch - EcRNase HI - NMR

 2zqb - SoRNase HI (mutant) - Shewanella oneidensis

2e4l - SoRNase HI

 3bsu - hRNase HI catalytic domain + RNA + DNA

 2ehg - RNase HI - Sulfolobus tokodaii

 1qhk - RNase HI N-terminal - yeast – NMR

RNase HII



3p83 - AfRNase HII + DNA polymerase sliding clamp - Archaeoglobus fulgidus

1i39, 1i3a - AfRNAse HII

3puf, 3p56, 3p5j - hRNAse H2 subunits α+β+γ 

3kio - mRNase H2 subunits α+β+γ 
- mouse

3o3g - TmRNase HII + DNA

 3o3f, 3o3h - TmRNase HII (mutant) + DNA

2etj - TmRNase HII 

1x1p - TkRNase HII

2dfe, 2dff, 2dfh - TkRNase HII (mutant) - Thermococcus kodakarensis

1eke - RNase HII - Methanocalcococcus jannaschii


2d0a, 2d0b, 2d0c - RNase HIII - Geobacillus stearothermophilus



RNase J

3bk1 - TtRNase J

3bk2 - TtRNase J + nucleotide




RNase LE

1dix - RNase LE - Solanum lycopersicum



RNase MS

1rms - RNase MS + nucleotide - Aspergillus phoenicis

RNase MC1

1v9h, 1j1f, 1j1g - McRNase MC1 (mutant) + nucleotide - Momordica charantia 

1ucd - McRNase MC1 + nucleotide


1bk7 - McRNase MC1



RNase NT

1vcz, 1vd1, 1vd3 - RNase NT + nucleotide] - Nicotiana glutinosa 



RNase P

3ok7, 3okb - TmRNase P + TmRNase P RNA + tRNA Phe

1nz0 - TmRNase P

1d6t - RNase P - Staphylococcus aureus

2a64 - RNase P (mutant) - Bacillus stearothermophilus



RNase PH

3dd6 - RNase PH - Bacillus anthracis

1oyp, 1oyr, 1oys - RNase PH - Bacillus subtilis 

1r6l, 1r6m - PaRNase PH - Pseudomonas aeruginosa

3b4t - MtRNase PH - Mycobacterium tuberculosis 

1udn - AaRNase PH

1udo, 1udq, 1uds - AaRNase PH (mutant)



RNase S

3oqy, 3oqz, 3or0, 1z3l, 1z3m, 1z3p, 1y92, 1y94, 1fev, 1d5d, 1d5e, 1d5h, 2rln - bRNase S seminal (mutant)

1tq9, 1r5c - bRNase S + nucleotide

 1r5d, 1r3m, 1n1x, 1n3z, 1j7z, 1j80, 1j81, 1j82, 1cjq, 1cjr, 1bsr - bRNase S


RNase S3

1iqq - RNase S3 - Japanese pear

RNase SA

3a5e, 1zgx, 1ynv, 1t2h, 1t2i, 1uci, 1ucj, 1uck, 1ucl, 1i70, 1i8v, 1box - SaRNase SA guanyl-specific (mutant) - Streptomyces aureofaciens

1lni - SaRNase SA
1gmp, 1gmq, 1gmr - SaRNase SA +nucleotide

 1ay7 - SaRNase SA + Barstar
1rsn - SaRNase SA + cyclophosphothiolate

RNase SA2

3dgy, 3dh2, 3d4a, 3d5g, 3d5i - SaRNase SA2 + mononucleotide

RNase SA3

1mgr, 1mgw - SaRNase SA3

RNase SF11



1ioo - RNase SF11 - Nicotiana alata



RNase T

2is3 - EcRNase T

2f96 - PaRNase T 



RNase T1

1tto - AoRNase T1 - Aspergillus oryzae 

1q9e, 1iyy, 1i2e, 1i2f, 1i2g, 1i3f, 1i3i, 1hz1, 1fys, 1fzu, 1ch0, 4bir, 3bir, 5bir - AoRNase T1 (mutant)

1lov, 1low, 1loy, 1i0v, 1i0x, 1b2m, 1rhl, 1bir, 1rgk, 1rgl - AoRNase T1 (mutant) + nucleotide
1bvi, 2bu4, 2hoh, 4hoh, 5hoh, 3hoh, 2gsp, 3gsp, 4gsp, 5gsp, 6gsp, 7gsp, 1gsp, 1det, 1rls, 1lra, 1rga - AoRNase T1 + nucleotide

 1ygw - AoRNase T1 – NMR

RNase U2

3agn, 3ago, 3ahw - UsRNase U2 + AMP - Ustilago sphaerogena

1rtu - UsRNase U2

RNase U2B

3ahs - UsRNase U2B

RNase Z

2e7y - TmRNase Z
2fk6 - BsRNase Z (mutant) + tRNA Thr

 1y44 - BsRNase Z (mutant)

Oligoribonuclease

2igi, 1yta – EcORNase

2gbz - ORNase - Xanthomonas campestris

1j9a - ORNase - Haemophilus influenzae

Polynucleotide Phosphorylase

3cdi - EcPNPase
3gll - EcPNPase core
3cdj - EcPNPase C-terminal truncated
1e3h, 1e3p - PNPase - Streptomyces antibioticus
3gcm, 3gme, 3h1c - EcPNPase + RNase E recognition domain
3h36 - PNPase fragment - Streptococcus mutans