Ribonuclease

From Proteopedia

Revision as of 07:55, 31 March 2011

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
 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

 -Eschericia coli

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 a+b+g 
 3kio - mRNase H2 subunits a+b+g 
- 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