ATPase

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   Print3D 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. ATPAse types include: F-ATPase - the prime producers of ATP; V-ATPase or Vacuolar-type H+ ATPase couples the energy to proton transport across membranes. A-ATPase are found in archaea; P-ATPase transport ions; E-ATPase hydrolyze extracellular ATP. 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. Central stalk in F(1)-ATPase is described in A-ATP Synthase. Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex (ATPase) RuvBL1 (RuvB-like 1; 2c9o ; 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, mutants of RuvBL1 and RuvBL2 with a two-thirds truncation of the flexible domain II were generated: RuvBL1deltaDII (R1∆DII) and RuvBL2deltaDII (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 dodecamer consisting of two heterohexameric rings with alternating RuvBL1 and RuvBL2 monomers (the RuvBL1 and the RuvBL2 monomers in the dodecamer are colored darkmagenta and cyan, respectively) bound to ADP/ATP (click on RuvBL1 or, alternatively on RuvBL2 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 43 % sequence identity and 65 % sequence similarity and therefore the 3D structures of R1deltaDII and R2deltaDII are very similar. 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 03-February-2015

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• F-ATPase
• F1F0 ATPase α subunit
  • P(1B)-Type Cu(I) Transporting ATPases ATP7A and ATP7B - bF1-ATPS+subunit O
    
  • Sodium-Potassium ATPase - F1-ATPS – Thermotoga maritima
• F1F0 ATPase β subunit
  • Esomeprazole and H+/K+ - ATPase Interaction – EcF1-ATPS membrane domain – Escherichia coli -NMR
    
  • Valosin Containing Protein D120 – EcF1-ATPS membrane domain + insertase YIDC – Cryo EM
    
  • A-ATP Synthase – EcF1-ATPS dimerization domain
    
  • 2c9o - EcF1-ATPS fragment – NMR
    
  • 1svm - F1-ATPS – NMR – tobacco
    
  • 4q4l - F1-ATPS – Burkholderia thailandensis
    
• F1F0 ATPase γ subunit
  • 1wu0 – BsATPS – NMR
    
  • 1a91, 1c0v, 1aty, 1c99 - EcF1-ATPS – NMR
    
  • 2wgm, 1yce – F0-ATPS – Ilyobacter tartaricus
    
  • 2x2v, 4cbk, 4cbj – F0-ATPS – Bacillus pseudofirmus
    
  • 4mjn - F1-ATPS - wheat
    
  • 4bem - F1F0-ATPS – Acetobacterium woodii
    
• F1F0 ATPase δ subunit
  • 1abv – EcF1-ATPS N terminal – NMR
    
• F1F0 ATPase ε subunit
  • 2rq6, 2rq7 - F1-ATPS – Thermosynechococcus elongatus
    
  • 1abv, 1aqt – 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,γ subunits
  • 1c17 – EcF1-ATPS – NMR
    
• 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, 2jiz, 4tt3, 4tsf – 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, 2f43 - F1-ATPS – rat
• F1F0 ATPase α,β,γ,δ subunits
  • 1qo1 - yF1-ATPS + protein 9
    
• F1F0 ATPase α,β,γ,ε subunits
  • 1jnv - EcF1-ATPS
    
  • 3oaa – EcF1-ATPS (mutant)
    
  • 2qe7 – F1-ATPS – Bacillus
    
• F1F0 ATPase α, β, γ, δ, ε subunits
  • 4asu, 2jdi, 2jj1, 2jj2 - bF1-ATPS
    
  • 2v7q, 1e79, 2ck3 - bF1-ATPS+inhibitor
    
  • 2xnd, 2xok - bF1-ATPS+ATPS lipid-binding protein
    
  • 2wpd, 2wss - yF1-ATPS+subunit 9+Mg+ADP+ATP - yeast
    
  • 3oe7, 3oee, 3oeh, 3ofn - yF1-ATPS (mutant)
    
  • 3fks, 3zry, 2hld - yF1-ATPS
    
  • 3zia - yF1-ATPS + inhibitor protein
    
  • 3j0j – TtATPS α,β,γ,δ,ε,ζ - Cryo EM
    
  • 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
    
  • 4f4s – yATPase subunit 9 + oligomycin
    
• 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)
    
  • 4o1s - ATPS subunit A – Thermoplasma volcanium
    
• 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 - sATPS subunit C - spinach
    
  • 2wie, 2xqs, 2xqt, 2xqu - ATPS subunit C – Arthrospira platensis
    
  • 3zk1, 3zk2 - ATPS subunit C – Fusobacterium nucleatum
    

V-ATPase subunit D+F

• • 4rnd – yATPase subunit D+F
    
• 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
    
• 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
    
  • 3wgv, 3wgu – pATPase + oligomycin
    
  • 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, 4ret, 4res, 4hyt, 4hqj - 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
    
  • 4h1w, 3w5a - rATPase+ sarcolipin
    
  • 3w5c, 3w5d, 1iwo - rATPase
    
  • 4bew - rATPase+ phosphate analog
    
  • 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
    
  • 4nab - rATPase Ca2E1 state (mutant) +AMPPCP
    
  • 1t5t - rATPase Ca2E1 state+ADP+AlF4
    
  • 1su4 - rATPase +2Ca2
    
  • 2by4, 2yfy, 3nal, 3nam, 3nan, 4uu1, 4uu0, 4j2t - rATPase HNE2 state+thapsigargin derivative
• Zn+2 transporting ATPase
  • 2ofg, 2ofh - sATPase N-terminal – NMR
    
  • 4umw, 4umv - ATPase +Mg – Shigella sonni
    
• 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
    

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Alexander Berchansky, Mark Hoelzer, Marius Mihasan, Jaime Prilusky, Karsten Theis, Michal Harel, Wayne Decatur