ATPase

From Proteopedia

Revision as of 09:20, 11 February 2014

spinqualitylabelsall models Human RuvB-like 1 dodecamer complex with ADP (PDB code 2c9o) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image ATPase is an enzyme which catalyzes the breakdown of ATP into ADP and a phosphate ion. This dephosphorylation releases energy which the enzyme uses to drive other reactions. Vacuolar-type H+ ATPase (V-ATPase) couples the energy to proton transport across membranes. ATPAse types include: F-ATPase - the prime producers of ATP; V-ATPase transport solutes; A-ATPase are found in archaea; P-ATPase transport ions; E-ATPase hydrolyze extracellular ATP. Vacuolar-type H+ ATPase couples the energy to proton transport across membranes. MipZ is an ATPase which forms a complex with the chromosome partitioning protein ParB and is responsible for the regulation of FtsZ ring formation. ATPase domains include metal-binding domain (MBD) and nucleotide-binding domain (NBD). For more details see: Cu transporting ATPase are in P(1B)-Type Cu(I) Transporting ATPases ATP7A and ATP7B. Na/K transporting ATPase are in Sodium-Potassium ATPase. H/K transporting ATPase are in Esomeprazole and H+/K+ ATPase Interaction. Transitional endoplasmic reticulum ATPase are in Valosin Containing Protein D120. A-ATP Synthase. Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex (ATPase)[1] (RuvB-like 1; 2c9o [2]; colored magenta) and its homolog RuvBL2 are evolutionarily highly conserved AAA+ ATPases essential for many cellular activities. They play an important role in chromatin remodeling, transcriptional regulation and DNA damage repair. RuvBL1 and RuvBL2 are overexpressed in different types of cancer and interact with major oncogenic factors, such as β-catenin and c-myc regulating their function. Since the full-length complex did not crystallize, were generated: (R1∆DII) and (R2∆DII). Crystals of the selenomethionine derivative of the R1∆DII/R2∆DII complex diffracted to 3 Å resolution and led to the determination of the three-dimensional structure of the complex. The structure reveals a (the RuvBL1 and the RuvBL2 are colored darkmagenta and cyan, respectively) bound to ADP/ATP (click on or, alternatively on to see protein/nucleotide interactions). The two heterohexamers interact with each other via the retained part of domain II, which is however poorly visible in the electron density maps, probably because the complex was not crystallized in a single conformational state. This is also hinted by evidence that in the RuvBL1 monomers, ATP was partly hydrolyzed to ADP. The dodecameric quaternary structure of the R1ΔDII/R2ΔDII complex observed in the crystal structure was confirmed by small-angle X-ray scattering analysis. RuvBL1 and RuvBL2 share . Due to the low data resolution, and even though the crystal structure could be solved by molecular replacement using a truncated RuvBL1 model, the use of a selenomethionine derivative was essential to elucidate the complex composition, since only one methionine residue is conserved out of 11 in R1ΔDII and 12 in R2ΔDII. Interestingly, truncation of domain II led to a substantial increase in ATP consumption of RuvBL1, RuvBL2 and their complex. In addition, we present evidence that DNA unwinding of the human RuvBL proteins can be auto-inhibited by domain II, which is not present in the homologous bacterial helicase RuvB. The alternation of charges in the central channel of the dodecamer shown below, combined with the diameter of the channel (ranging between 17 and 21 Å) suggests interactions with single-stranded nucleic acids. Electrostatic potential mapped at the molecular surface for the R1deltaDII/R2deltaDII dodecamer. (a) top view and (b) cross-section view showing the central channel. (c) cross-section view of the SV40 Ltag hexamer complexed with ATP (PDB 1svm), included for comparison. In (a) and (b) the R1deltaDII and R2deltaDII monomers are colored gold and cyan, respectively. In (c) the SV40 monomers are alternately colored gold and cyan. Our data give new insights into the molecular arrangement of RuvBL1 and RuvBL2 and strongly suggest that in vivo activities of these highly interesting therapeutic drug targets are regulated by cofactors inducing conformational changes via domain II in order to modulate the enzyme complex into its active state.

3D Structures of ATPase

Updated on 11-February-2014

F-ATPase

F1F0 ATPase α subunit

2jmx - bF1-ATPS+subunit O
2r9v - F1-ATPS – Thermotoga maritima

F1F0 ATPase β subunit

1b9u – EcF1-ATPS membrane domain – Escherichia coli -NMR
1l2p – EcF1-ATPS dimerization domain
2khk - EcF1-ATPS fragment – NMR

F1F0 ATPase γ subunit

1wu0 – BsATPS – NMR
1a91, 1c0v, 1aty, 1c99 - EcF1-ATPS – NMR
2wgm, 1yce – F0-ATPS – Ilyobacter tartaricus
2x2v – F0-ATPS – Bacillus pseudofirmus

F1F0 ATPase δ subunit

1abv – EcF1-ATPS N terminal – NMR

F1F0 ATPase ε subunit

2rq6, 2rq7 - F1-ATPS – Thermosynechococcus elongatus
1abv– EcF1-ATPS (mutant)
1bsh, 1bsn – EcF1-ATPS – NMR
2e5t, 2e5u – BsF1-ATPS C terminal – NMR
2e5y – BsF1-ATPS

F1F0 ATPase α, β subunits

1sky – BsF1-ATPS – Bacillus sp. Ps3

F1F0 ATPase α, δ subunits

2a7u – EcF1-ATPS N termini – NMR

F1F0 ATPase β, δ subunits

2cly – bF1-ATPS + ATPS coupling factor

F1F0 ATPase γ, ε subunits

1fs0 – EcF1-ATPS

F1F0 ATPase α, β, γ subunits

1ohh – bF1-ATPS+ IF1 inhibitor – bovine
1e1q, 2w6e, 2w6f, 2w6g, 2w6h, 2w6i, 2w6j - bF1-ATPS
1e1r - bF1-ATPS+Mg+ADP+AlF4
1w0j, 1w0k - bF1-ATPS+BeF3
1nbm - bF1-ATPS+nitrobenzofurazan
1mab - F1-ATPS – rat

F1F0 ATPase α, β, γ, δ, ε subunits

4asu - bF1-ATPS
2v7q - bF1-ATPS+inhibitor
2xnd, 2xok - bF1-ATPS+ATPS lipid-binding protein
2wpd, 2wss - yF1-ATPS+subunit 9+Mg+ADP+ATP
3oe7, 3oee, 3oeh, 3ofn - yF1-ATPS (mutant)
3fks, 3zry - yF1-ATPS
3j0j – TtATPS α,β,γ,δ,ε,ζ - Cryo EM

F1F0 ATPase α, β, γ, ε subunits

3oaa – EcF1-ATPS (mutant)
1e79 - bF1-ATPS

F1F0 ATPase α,β,γ,δ,ε,9,B,D,6,O subunits

4b2q – yATPase subunits α,β,γ,δ,ε +9,B,D,6,O – Cryo EM

1bmf - bF1-ATPS
3dze – bF1-ATPS subunit S
1cow - bF1-ATPS+aurovertin B

V-ATPase

V-ATPase subunit A

3i4l - PhATPS subunit A+AMPPNP
3mfy, 3m4y, 3nd8, 3nd9, 3p20, 3qg1, 3qia, 3qjy, 3sdz, 3se0 - PhATPS subunit A mutant)
3i72, 3i73, 3ikj - TtATPS subunit A (mutant)

V-ATPase subunit B

2c61 - MmATPS subunit B – Methanosarcina mazei
2rkw, 3b2q, 3ssa, 3tgw, 3tiv - MmATPS subunit B (mutant)
3dsr - MmATPS subunit B+ADP
3eiu - MmATPS subunit B+ATP

V-ATPase subunit C

1u7l, 3u2f, 3u2y, 3u32, 3ud0 - yATPS subunit C
3v3c - ATPS subunit C - pea
1ijp, 1l6t – EcF1-ATPS subunit C (mutant) – Escherichia coli - NMR
1r5z, 1v9m - TtATPS subunit C – Thermus thermophilus
3lg8 - MtATPS subunit C C-terminal
2w5j - ATPS subunit C - spinach

V-ATPase subunit E

2kz9 – yATPase subunit E
2dm9, 2dma, 4dt0 - PhATPS subunit E – Pyrococcus horikoshii
2kk7 - MjATPS subunit E – Methanocaldococcus jannaschii
3v6i – TtATPS subunit E + VAPC

V-ATPase subunit F

2qai - ATPS subunit F – Pyrococcus furiosus
2i4r - ATPS subunit F – Archaeoglobus fulgidus
2ov6 - MmATPS subunit F - NMR
2d00 - TtATPS subunit F
4ix9 – yATP subunit F (mutant)

V-ATPase subunit G

2k88 - yATPS subunit G - NMR

V-ATPase subunit H

1ho8 – yATPS subunit H – yeast

V-ATPase subunit K

2bl2, 2cyd - ATPS subunit K – Enterococcus hirae

V-ATPase subunit I

3rrk – ATPS subunit I N terminal – Meiothermus ruber

4dl0, 4efa - yATPase subunits C,G,E
3w3a - yATPS subunit A,B,D,F
3a5c, 3a5d - TtATPS subunit A,B,D,F
3gqb - TtATPS subunit A (mutant),B (mutant)
3k5b - TtATPS subunit E (mutant)+C

P-ATPase

Cu transporting ATPase

2kmv, 2kmx, 2arf – hATPase NBD – human – NMR
2kij - hATPase actuator domain – NMR
1yjr, 1yjt, 1yju, 1yjv - hATPase (mutant) 6th soluble domain – NMR
1y3j, 1y3k - hATPase 5th soluble domain – NMR
1s6o, 1s6u - hATPase 2nd soluble domain – NMR
1q8l - hATPase 2nd MBD – NMR
1aw0, 2aw0 - hATPase 4th MBD – NMR
1kvi, 1kvj - hATPase 1st MBD – NMR
3dxs - AtATPase MBD – Arabidopsis thaliana
3voy - AfATPase – Archaeoglobus fulgidus – CryoEM
3skx, 3sky - AfATPase NBD
2k1r - hATPase MBD+ ATOX1 – NMR
2rop, 2g9o, 2ga7 - hATPase MBD – NMR
2rml - BsATPase N-terminal – Bacillus subtilis – NMR
2gcf - sATPase N-terminal - Synechocystis – NMR
4a48 - sATPase
2iye - SsATPase catalytic domain – Sulfolobus solfataricus
2yj3 - SsATPase catalytic domain (mutant)
2yj4, 2yj5, 2yj6 - SsATPase catalytic domain (mutant) + nucleotide
1fvq, 1fvs - hATPase – NMR
3cjk – hATPase + Cu transporting protein ATX1
3rfu – ATPase – Legionella pneumophila
4f2f - ATPase metal-binding domain – Streptococcus pneumonia
3j08, 3j09 - AfATPase
3a1c – AfATPase + AMPPCP
3a1d - AfATPase + ADP-Mg
3a1e - AfATPase (mutant) + AMPPCP

Na/K transporting ATPase

3a3y - SaATPase+K+ouabain – Squalus acanthias
3kdp, 3b8e – pATPase – pig
3n23 – pATPase + ouabain
3b8e - pATPase a+BeF3
2hc8 –AfATPase CopA A domain
2b8e - AfATPase CopA NBD
2xze - SaATPase
1mo8, 1mo7 - ATPase α-1 – rat
1q3i - pATPase NBD
3n2f - pATPase subunits α,β,γ
2zxe - ATPase subunits α,β + phospholemman-like protein – spiny dogfish

Ca+2 transporting ATPase

3fgo - rATPase+CPA+AMPPCP – rabbit
3b9r, 1xp5 - rATPase+AlF4
1wpg - rATPase+MgF4
3w5b - rATPase+Mg
3w5c, 3w5d, 1iwo - rATPase
2zbe, 3b9b – rATPase+BeF3
2zbf - rATPase+BeF3+TG
2zbg - rATPase+AlF4+TG
2zbd, 3ar8 - rATPase+AlF4+nucleotide+Ca
3ar9 - rATPase+BeF3+nucleotide
2dqs, 3ar2, 1vfp - rATPase+AMPPCP
2c88, 2c8k, 3ar4, 3ar3, 3ar5, 3ar7 - rATPase+nucleotide+TG
2ear, 2c8l - rATPase+TG
2agv - rATPase+TG+BHQ
2eas - rATPase+CPA
2eat - rATPase+CPA+GT
3ar6 - rATPase+TNP-ADP+GT
2eau - rATPase+CPA+curcumin
3ba6 - rATPase phosphoenzyme intermediate
3fpb - rATPase+ATP+cyclopiazonic acid
3fps, 2oa0 - rATPase+ADP+cyclopiazonic acid
2o9j - rATPase+MgF4+cyclopiazonic acid
1kju, 3n5k - rATPase E2 state
2c9m - rATPase Ca2E1 state
1t5s, 3n8g - rATPase Ca2E1 state+AMPPCP
1t5t - rATPase Ca2E1 state+ADP+AlF4
1su4 - rATPase +2Ca2
2by4, 2yfy, 3nal, 3nam, 3nan - rATPase HNE2 state+thapsigargin derivative

Zn+2 transporting ATPase

2ofg, 2ofh - sATPase N-terminal – NMR

K+ transporting ATPase

2a00, 2a29 - EcATPase NBD of KdpB+AMPPNP– Escherichia coli – NMR
1svj, 1u7q - EcATPase NBD of KdpB – NMR
2ynr – pATPase – Cryo EM

As+ transporting ATPase

1ii0, 1f48 - EcATPase
1ihu – EcATPase+Mg+ADP+AlF3
1ii9 - EcATPase
3h84, 3idq, 3a36, 3a37 - yATPase GET3 – yeast
3sja, 3sjb, 3sjc, 3sjd, 3zs8, 3zs9, 3b2e, 3vlc - yATPase GET3 + GET1 cystolic domain
3ibg - ATPase GET3 – Aspergillus fumigatus

H+ transporting ATPase

3b8c - AtATPase C terminal truncated
1mhs - ATPase – Neurospora crassa

Na+ transporting ATPase

2db4, 3aou - EhATPase subunit K – Enterococcus hirae
3aon - EhATPase subunits D,G
3vr2 - EhATPase subunits A,B
3vr4, 3vr5 - EhATPase subunits A,B,D,G
3vr3 - EhATPase subunits A,B + AMPPNP
3vr6 - EhATPase subunits A,B,D,G + AMPPNP
1yce - ATPase rotor ring – Ilyobacter tartaricus

H/K transporting ATPase

1iwc, 1iwf - pATPase NBD
3ixz - pATPase a+AlF4
2xzb – pATPase subunits α, β

Mg+2 transporting ATPase

3gwi – EcATPase P-1 NBD

Arg/ornithine transporting ATPase

3md0 – MtATPase+GDP – Mycobacterium tuberculosis
1kmh - ATPase alpha subunit+tentoxin – spinach
1h8e – cATPase+ADP+AlF4+ADP+SO4 - cow
1h8h - cATPase+ AMPPNP
1efr - cATPase+efrapeptin
3fks – ATPase – yeast
3ea0 – ATPase ParA, fragment – Chlorobium tepidum
2qen – ATPase (mutant) Walker-type – Pyrococcus abyssi
3cf0, 3cf1, 3cf3 – mATPase NBD+ADP – mouse
3cf2 - mATPase NBD+ADP+AMP-PNP
2r31, 2p4x – PdATPase ATP12 – Paracoccus denitrificans
2zd2 – PdATPase (mutant) ATP12
1d8s – EcATPase F1
1vdz – PhATPase subunit A – Pyrococcus horikoshii

RNA-dependent ATPase

3eaq, 3i31, 3i32 – TtATPase fragment
3mwj – TtATPase N-terminal (mutant)
3mwk, 3nbf – TtATPase N-terminal + 8-oxo-AMP
3mwl - TtATPase N-terminal (mutant) + 8-oxoadenine
3nej - TtATPase reca-like domain (mutant)

Proteasome-associated ATPase

3fp9, 3m9b, 3m9h – MtATPase intern domain
3m91, 3m9d - MtATPase coiled coil domain + protein PUP
3kw6 – hATPase 5

Transitional endoplasmic reticulum ATPase

3hu1, 3hu2, 3hu3 – hTer-ATPase + ATPGS
3qc8, 3qq8, 3qwz - hTer-ATPase N terminal + FAS-associated factor 1
3qq7 - hTer-ATPase N terminal
3tiw - hTer-ATPase N terminal + E3 ubiquitin-protein ligase peptide

LAO/AO transport system ATPase

3nxs – ATPase – Mycobacterium smegmatis

DNA double-strand repair ATPase (Rad50)

3aux – MjRad50 – Methanocaldococcus jannaschii
3auy - MjRad50 + ADP
3av0 - MjRad50 + ATP
3qg5 – Rad50 NBD + MRE11 – Thermotoga maritima
3qkr, 3qks, 3qf7 - PfRad50 NBD + MRE11 – Pyrococcus furiosus
3qkt - PfRad50 NBD + AMPPNP
3qku - PfRad50 NBD + AMPPNP + MRE11

MipZ ATPase

2xit, 2xj4 – CcMipZ – Caulobacter crescentus
2xj9 – CcMipZ (mutant)

3nbx – EcATPase Rava + ADP

FlaI ATPase

4ihq, 4ii7 – ATPase (mutant) – Sulfolobus acidocaldarius

References

1. ↑ Gorynia S, Bandeiras TM, Pinho FG, McVey CE, Vonrhein C, Round A, Svergun DI, Donner P, Matias PM, Carrondo MA. Structural and functional insights into a dodecameric molecular machine - The RuvBL1/RuvBL2 complex. J Struct Biol. 2011 Sep 10. PMID:21933716 doi:10.1016/j.jsb.2011.09.001
2. ↑ Matias PM, Gorynia S, Donner P, Carrondo MA. Crystal structure of the human AAA+ protein RuvBL1. J Biol Chem. 2006 Dec 15;281(50):38918-29. Epub 2006 Oct 23. PMID:17060327 doi:10.1074/jbc.M605625200