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. For more details on RNase A see:
For RNase B and RNase S see RNaseS RNaseB.
Active Site of Ribonuclease A[1]
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves RNA strands best next to cytidine and uridine nucleotides--the reason for this may be seen in a . Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.
3D Structures of Ribonuclease
Update June 2012
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, 1afu, 1bel, 1c0b, 1c0c, 1lsq, 1rat, 1rbn, 1rha, 1rhb, 1rnx, 1rny, 1rsm, 1xps, 1xpt, 2g8q, 2rat, 3mzq, 3mzr, 3rat, 3rn3, 4rat, 5rat, 6rat, 7rat, 7rsa, 8rat, 8rsa, 9rat, 9rsa, 3mwr- 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,1a5p, 1a5q, 1c9v, 1c9x, 3rsp, 4rsd, 3ql1, 3ql2, 3rh1, 3rid - 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,1afk, 1afl, 1eos, 1eow, 1o0h, 1o0m, 1o0n, 1o0o, 1qhc, 1rcn- 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, 3qsk - 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
2bex - hRNase 2 + RNase inhibitor protein
2bzz, 2c01, 2c02, 2c05 - hRNase 2 + inhibitor
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
1t4n, 1t4o - yRNase III – yeast - NMR
2lbs - yRNase III RNA-binding domain + RNA – NMR
2kb5 - hRNase 3 - NMR
1dyt, 1qmt - hRNase 3
1h1h - hRNase 3 + nucleotide
2khx – hRNase III
3n3w, 3o2r - RNase III nuclease domain – Campylobacter jejuni
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 6
1oj1, 1oj8 – BuRNase + nucleotide
RNase 7
2hky - hRNase 7 - NMR
RNase A
1rra - RNase A (mutant) – rat
1rta - bRNase A
RNase B
1rbb – bRNase B
1rbj - bRNase B + tetranucleotide
RNase BA
1x1u, 1x1x, 1x1y, 1b27, 1b2u, 1b3s, 1x1w - 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 F1
1fus, 1fut – GfRNase F1 + nucleotide – Gibberella fujikuroi
1rck, 1rcl - GfRNase F1 - NMR
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
1rbr, 1rbs, 1rbt, 1rbu, 1rbv, 2rn2 - EcRNase H
1lav, 1law, 1rda, 1rdb, 1rdc - EcRNase H (mutant)
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
3ey1, 3i8d - BhRNase H (mutant) + D
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, 1rnh - 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 - yRNase HI N-terminal – NMR
3u3g – Rnase HI – uncultured organism
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, 1io2 - TkRNase HII
2dfe, 2dff, 2dfh - TkRNase HII (mutant) - Thermococcus kodakarensis
1eke - RNase HII - Methanocalcococcus jannaschii
RNase HIII
2d0a, 2d0b, 2d0c - GsRNase HIII - Geobacillus stearothermophilus
3asm - GsRNase HIII (mutant)
1uax - PhRNase HIII – Pyrococcus horikoshii
RNase J
3bk1 - TtRNase J
3bk2 - TtRNase J + nucleotide
3zq4 - BsRNase J1- Bacillus subtilis
RNase LE
1dix - RNase LE - Solanum lycopersicum
RNase MAR1
1xn4 - RNase MAR1 – Leishmania major
2b34 - RNase MAR1 – Caenorhabditis elegans
RNase MS
1rms, 1rds - RNase MS + nucleotide - Aspergillus phoenicis
RNase MC1
1v9h, 1j1f, 1j1g - McRNase MC1 (mutant) + nucleotide - Momordica charantia
1ucg - McRNase MC1 (mutant)
1ucd, 1uca, 1ucc - McRNase MC1 + nucleotide
1bk7 - McRNase MC1
RNase NT
1vcz, 1vd1, 1vd3 - NgRNase NT + nucleotide] - Nicotiana glutinosa
1iyb - NgRNase NW
RNase P
3ok7, 3okb, 3q1q, 3q1r - TmRNase P + TmRNase P RNA + tRNA Phe
1nz0 - TmRNase P
1d6t - RNase P - Staphylococcus aureus
2a64 - RNase P (mutant) - Bacillus stearothermophilus
1a6f, 1nbs - BsRNase P (mutant)
1ts9, 1tsf – AfRNase P
1u9s – RNase P – synthetic
2avs - PfRNase P (mutant) – Pyrococcus furiosus
2k3r, 2ki7 - PfRNase P
2cvz, 2zae – PhRNase P
3iab – yRNase P subunits POP6 POP7 + RNase MRP P3 domain
RNase PH
3dd6 - RNase PH - Bacillus anthracis
1oyp, 1oyr, 1oys - BsRNase PH
1r6l, 1r6m - PaRNase PH - Pseudomonas aeruginosa
3b4t - MtRNase PH - Mycobacterium tuberculosis
1udn - AaRNase PH
1udo, 1udq, 1uds - AaRNase PH (mutant)
RNase RH
1bol – Rhizopus niveus
RNase S
3oqy, 3oqz, 3or0, 1z3l, 1z3m, 1z3p, 1y92, 1y94, 1fev, 1d5d, 1d5e, 1d5h, 2rln, 1qwq - bRNase S seminal (mutant)
1tq9, 1r5c, 11ba, 11bg - bRNase S + nucleotide
1r5d, 1r3m, 1n1x, 1n3z, 1j7z, 1j80, 1j81, 1j82, 1cjq, 1cjr, 1bsr,1rbc, 1rbd, 1rbe, 1rbf, 1rbg, 1rbh, 1rbi, 1rnu, 1rnv, 2rns - bRNase S
1b6v - bRNase S/bRNase A
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,1c54, 1rge, 1rgf, 1rgg, 1rgh, 1sar - SaRNase SA
1gmp, 1gmq, 1gmr, 2sar - SaRNase SA +nucleotide
1ay7 - SaRNase SA + Barstar
1rsn - SaRNase SA + cyclophosphothiolate
RNase SA2
1py3, 1pyl - SaRNase 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
3ngy – EcRNase T (mutant) + His tag
3ngz - EcRNase T (mutant) + nucleotide
3nh0, 3nh1, 3nh2 - EcRNase T + nucleotide
RNase T1
1tto,1rn1, 1rn4, 1rnt, 2aad, 2aae - AoRNase T1 - Aspergillus oryzae
1q9e, 1iyy, 1i2e, 1i2f, 1i2g, 1i3f, 1i3i, 1hz1, 1fys, 1fzu, 1ch0, 4bir, 3bir, 5bir,1g02, 1hyf, 1trp, 1trq, 2bir, 4rnt, 5rnt, 6rnt, 7rnt , 8rnt, 9rnt - 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,1bu4, 1rgc, 2rnt, 3bu4, 4bu4, 5bu4, 3syu, 3urp - AoRNase T1 + nucleotide
3rnt - AoRNase T1 + V
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)
2cbn – EcRNase Z
RNase α-sarcin
1de3 - αsRNase – Aspergillus giganteus
1r4y - αsRNase (mutant)
Oligoribonuclease
2igi, 1yta – EcORNase
2gbz - ORNase - Xanthomonas campestris
1j9a - ORNase - Haemophilus influenzae
3tr8 – ORNase – Coxiella burnetii
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
Binase
1gou, 1gov, 1goy – BiBinase – Bacillus intermedius
2rbi – BiBinase (mutant)
Poly(A)-specific RNase
1ug8 – mParn R3H domain - NMR
1whv – mParn RNA-binding domain - NMR
2rok - mParn CAP-binding domain - NMR
3d45 - mParn + nucleotide
2a1s - hParn
2a1r, 3ctr – hParn + nucleotide
2zpo – RNase – Chelonia mydas
3a4y, 3idz, 3ie0, 3ie2 – TtRNase (mutant) – Thermus thermophilus
3iek - TtRNase
3ie1, 3iem - TtRNase (mutant) + RNA
3iel - TtRNase + nucleotide
