Ribonuclease

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 5 is known as angiogenin and is a potent stimulator of new blood vessels formation. 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:

• RNase A
  
• Ribonuclease A Catalysis
  
• RNase A Oligomers
  
• RNase A NMR
  
• User:R. Jeremy Johnson/RNaseA
  
• RNaseA Nobel Prizes.
  

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 – Zebra fish
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, 1b1e, 1b1j, 1k59, 1k5a, 1k5b - hRNase 5 (mutant)

1ang, 1b1i, 2ang - hRNase 5
1awz - hRNase 5 - NMR
1a4y - hRNase 5 + RNAse inhibitor 1agi - bRNase 5
1h53, 1hby - hRNase 5 + phosphate derivative
1gio - bRNase 5 - NMR
1h53 - hRNase 5 + PO4< br / > 1h0d - hRNase 5 + antibody
3lje - ZeRNase 5
2bwk - mRNase 5 + sulfate - mouse
2bwl - mRNase 5 + phosphate
2j4t - mRNase 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