Enzyme Nomenclature

Continued from EC 3.6.3

EC 3.6.4 Acting on acid anhydrides; involved in cellular and subcellular movement

Contents

EC 3.6.4.1 myosin ATPase
EC 3.6.4.2 dynein ATPase
EC 3.6.4.3 now EC 5.6.1.1
EC 3.6.4.4 plus-end-directed kinesin ATPase
EC 3.6.4.5 minus-end-directed kinesin ATPase
EC 3.6.4.6 vesicle-fusing ATPase
EC 3.6.4.7 peroxisome-assembly ATPase
EC 3.6.4.8 proteasome ATPase
EC 3.6.4.9 chaperonin ATPase
EC 3.6.4.10 non-chaperonin molecular chaperone ATPase
EC 3.6.4.11 deleted
EC 3.6.4.12 DNA helicase
EC 3.6.4.13 RNA helicase


Entries

EC 3.6.4.1

Accepted name: myosin ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name: actomyosin

Systematic name: ATP phosphohydrolase (actin-translocating)

Comments: Proteins of the contractile apparatus of muscle and nonmuscle cells; myosin molecule consists of two heavy chains (about 200 kDa) and two pairs of light chains (15-27 kDa). The head region of the heavy chain contains actin- and ATP-binding sites. ATP hydrolysis provides energy for actomyosin contraction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Rayment, I. The structural basis of myosin ATPase activity. J. Biol. Chem. 271 (1996) 15850-15853. [PMID: 8663496]

2. Hasson, T. and Mooseker, M.S. Vertebrate unconventional myosins. J. Biol. Chem. 271 (1996) 16431-16434. [PMID: 8690736]

3. Murphy, C.T. and Spudich, J.A. The sequence of the myosin 50-20K loop affects myosin's affinity for actin throughout the actin-myosin ATPase cycle and its maximum ATPase activity. Biochemistry 38 (1999) 3785-3792. [PMID: 10090768]

[EC 3.6.4.1 created 1984 as EC 3.6.1.32, transferred 2000 to EC 3.6.4.1]

EC 3.6.4.2

Accepted name: dynein ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): dynein adenosine 5'-triphosphatase

Systematic name: ATP phosphohydrolase (tubulin-translocating)

Comments: A multisubunit protein complex associated with microtubules. Hydrolysis of ATP provides energy for the movement of organelles (endosomes, lysosomes, mitochondria) along microtubules to the centrosome towards the microtubule's minus end. It also functions in the movement of eukaryotic flagella and cilia. It consists of two heavy chains (about 500 kDa), three-four intermediate chains (about 70 kDa) and four light chains (about 50 kDa).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Summers, K.E. and Gibbons, I.R. Adenosine triphosphate-induced sliding of tubules in trypsin-treated flagella of sea-urchin sperm. Proc. Natl. Acad. Sci. USA 68 (1971) 3092-3096. [PMID: 5289252]

2. Gibbons, I.R. Dynein ATPases as microtubule motors. J. Biol. Chem. 263 (1988) 15837-15840. [PMID: 2972702]

3. Gee, M. and Vallee, R. The role of the dynein stalk in cytoplasmic and flagellar motility. Eur. Biophys. J. 27 (1998) 466-473. [PMID: 9760728]

[EC 3.6.4.2 created 1984 as EC 3.6.1.33, transferred 2000 to EC 3.6.4.2]

[EC 3.6.4.3 Transferred entry: microtubule-severing ATPase. Now EC 5.6.1.1, microtubule-severing ATPase (EC 3.6.4.3 created 2000 as 3.6.4.3, deleted 2018)]

EC 3.6.4.4

Accepted name: plus-end-directed kinesin ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): kinesin

Systematic name: kinesin ATP phosphohydrolase (plus-end-directed)

Comments: Microtubular motor protein, involved in organelle movement, in mitosis and meiosis. In contrast to dynein, it moves along microtubules towards the plus end. Composed of two heavy (α) chains (110 kDa) and two or more light (β) chains (65-75 kDa). Also hydrolyses GTP.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Vale, R.D., Reese, T.S. and Sheetz, M.P. Identification of a novel force-generating protein, kinesin, in microtubule-based motility. Cell 42 (1985) 39-50. [PMID: 3926325]

2. Howard, J. Molecular motors: structural adaptations to cellular functions. Nature 389 (1997) 561-567. [PMID: 9335494]

3. Nakagawa, T., Tanaka, Y., Matsuoka, E., Kondo, S., Okada, Y., Noda, F., Kanai, Y. and Hirokawa, N. Identification and classification of 16 new kinesin superfamily (KIF) proteins in mouse genome. Proc. Natl. Acad. Sci. USA 94 (1997) 9654-9659. [PMID: 9275178]

[EC 3.6.4.4 created 2000]

EC 3.6.4.5

Accepted name: minus-end-directed kinesin ATPase

Reaction: ATP + H2O = ADP + phosphate

Systematic name: kinesin ATP phosphohydrolase (minus-end-directed)

Comments: Structurally almost identical to EC 3.6.4.3 (microtubule-severing ATPase) but the movement it catalyses is towards the minus end of microtubules.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Henningsen, U. and Schliwa, M. Reversal in the direction of movement of a molecular motor. Nature 389 (1997) 93-96. [PMID: 9288974]

2. Sharp, D.J., Kuriyama, R., Essner, R. and Baas, P.W. Expression of a minus-end-directed motor protein induces Sh9 cells to form axon-like processes with uniform microtubule polarity orientation. J. Cell Sci. 110 (1997) 2373-2380. [PMID: 9410876]

3. Sablin, E.P., CASe, R.B., Dai, S.C., Hart, C.L., Ruby, A., Vale, R.D. and Fletterick, R.J. Direction determination in the minus-end-directed kinesin motor ncd. Nature 395 (1998) 813-816. [PMID: 9796817]

[EC 3.6.4.5 created 2000]

EC 3.6.4.6

Accepted name: vesicle-fusing ATPase

Reaction: ATP + H2O = ADP + phosphate

Systematic name: ATP phosphohydrolase (vesicle-fusing)

Comments: A large family of ATP-hydrolysing enzymes involved in the heterotypic fusion of membrane vesicles with target membranes and the homotypic fusion of various membrane compartments. They belong to the AAA-type (ATPase associated with a variety of cell activities) ATPase superfamily. They include peroxin, which apparently is involved in Zellweger's syndrome.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Confalonieri, F. and Duguet, M. A 200-amino acid ATPase module in search of a basic function. BioEssays 17 (1995) 639-650. [PMID: 7646486]

2. Imamura, A., Tamura, S., Shimoyawa, N., Suzuki, Y., Zhang, Z., Tsukamoto, T., Orii, T., Kondo, N., Osumi, T. and Fujiki, Y. Temperature-sensitive mutation in PEX1 moderates the phenotypes of peroxisome deficiency disorders. Hum. Mol. Genet. 7 (1998) 2089-2094. [PMID: 9817926]

3. Babst, W., Wendland, B., Estepa, E.J. and Emr, S.D. The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function. EMBO J. 17 (1998) 2982-2983. [PMID: 9606181]

[EC 3.6.4.6 created 2000]

EC 3.6.4.7

Accepted name: peroxisome-assembly ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): peroxisome assembly factor-2

Systematic name: ATP phosphohydrolase (peroxisome-assembling)

Comments: An extremely diversified group of enzymes that use the energy of ATP hydrolysis to import and assemble peroxisome components into the organelle. Their molecular masses range from 25 to 600 kDa.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lee, Y.J. and Wickner, R.B. AFG1, a new member of the SEC18-NSF, PAS1, CDC48-VCP, TBP family of ATPases. Yeast 8 (1992) 787-790. [PMID: 1441755]

2. Tsukamoto,T., Miura, S., Nakai, T., Yokota, S., Shimozawa, N., Suzuki, Y., Orii, T., Fujiki, Y., Sakai, F., Bogaki, A., Yasumo, H. and Osumi, T. Peroxisome assembly factor-2, a putative ATPase cloned by functional complementation on a peroxisome-deficient mammalian cell mutant. Nat. Genet. 11 (1995) 395-401. [PMID: 7493019]

3. Yahraus, T., Braverman, N., Dodt, G., Kalish, J.E., Morrell, J.C., Moser, H.W., Valle, D. and Gould, S.J. The peroxisome biogenesis disorder group 4 gene, PXAAA1, encodes a cytoplasmic ATPase required for stability of the PTS1 receptor. EMBO J. 15 (1996) 2914-2923. [PMID: 8670792]

[EC 3.6.4.7 created 2000]

EC 3.6.4.8

Accepted name: proteasome ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name: RP triple-A protein; RP triphosphatase

Systematic name: ATP phosphohydrolase (polypeptide-degrading)

Comments: Belongs to the AAA-type superfamily and, like EC 3.6.4.5 (minus-end-directed kinesin ATPase), is involved in channel gating and polypeptide unfolding before proteolysis in the proteasome. Six ATPase subunits are present in the regulatory particle (RP) of 26S proteasome.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Rivett, A.J., Mason, G.G., Murray, R.Z. and Reidlinger, J. Regulation of proteasome structure and function. Mol. Biol. Rep. 24 (1997) 99-102. [PMID: 9228289]

2. Mason, G.G., Murray, R.Z., Pappin, D. and Rivett, A.J. Phosphorylation of ATPase subunits of the 26S proteasome. FEBS Lett. 430 (1998) 269-274. [PMID: 9688553]

[EC 3.6.4.8 created 2000]

EC 3.6.4.9

Accepted name: chaperonin ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): chaperonin

Systematic name: ATP phosphohydrolase (polypeptide-unfolding)

Comments: Multisubunit proteins with 2x7 (Type I, in most cells) or 2x8 (Type II, in Archaea) ATP-binding sites involved in maintaining an unfolded polypeptide structure before folding or entry into mitochondria and chloroplasts. Molecular masses of subunits ranges from 10-90 kDa. They are a subclass of molecular chaperones that are related to EC 3.6.4.8 (proteasome ATPase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Hemmingsen, S.M., Woolford, C., van der Vies, S.M., Tilly, K., Dennis, D.T., Georgopoulos, G.C., Hendrix, R.W. and Ellis, R.J. Homologous plant and bacterial proteins: chaperone oligomeric protein assembly. Nature 333 (1988) 330-334. [PMID: 2897629]

2. Lubber, T.H., Donaldson, G.K., Viitanen, P.V. and Gatenby, A.A. Several proteins imported into chloroplasts form stable complexes with the GroEL-related chloroplast molecular chaperone. Plant Cell 1 (1989) 1223-1230.

3. Ellis, R.J. (Ed.), The Chaperonins, Academic Press, San Diego, 1996.

4. Ranson, N.A., White, H.E. and Saibil, H.R. Chaperonins. Biochem. J. 333 (1998) 233-242. [PMID: 9657960]

[EC 3.6.4.9 created 2000]

EC 3.6.4.10

Accepted name: non-chaperonin molecular chaperone ATPase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): molecular chaperone Hsc70 ATPase

Systematic name: ATP phosphohydrolase (polypeptide-polymerizing)

Comments: This is a highly diverse group of enzymes that perform many functions that are similar to those of chaperonins. They comprise a number of heat-shock-cognate proteins. They are also active in clathrin uncoating and in the oligomerization of actin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Sadis, S. and Hightower, L.E. Unfolded proteins stimulate molecular chaperone Hsc70 ATPase by accelerating ADP/ATP exchange. Biochemistry 31 (1992) 9406-9412. [PMID: 1356434]

2. Blond-Elquindi, S., Fourie, A.M., Sambrook, J.F. and Gething, M.J. Peptide-dependent stimulation of the ATPase activity of the molecular chaperone BiP is the result of conversion of oligomers to active monomers. J. Biol. Chem. 268 (1993) 12730-12735. [PMID: 8509407]

3. Wawrzynow, A., Wojtkowiak, D., Marszalek, J., Banecki, B., Jonsen, M., Graves, B., Georgopoulos, C. and Zylicz, M. The ClpX heat-shock protein of Escherichia coli, the ATP-dependent substrate specificity component of the ClpP-ClpX protease, is a novel molecular chaperone. EMBO J. 14 (1995) 1867-1877. [PMID: 7743994]

4. Sriram, M., Osipiuk, J., Freeman, B., Morimoto, R. and Joachimiak, A. Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain. Structure 5 (1997) 403-414. [PMID: 9083109]

5. Li, X., Su, R.T., Hsu, H.T. and Sze, H. The molecular chaperone calnexin associated with the vacuolar H+-ATPase from oat seedlings. Plant Cell 10 (1998) 119-130. [PMID: 9477575]

[EC 3.6.4.10 created 2000]

[EC 3.6.4.11 Deleted entry: nucleoplasmin ATPase. The activity has been shown not to take place. (EC 3.6.4.11 created 2000, deleted 2018)]

EC 3.6.4.12

Accepted name: DNA helicase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): 3' to 5' DNA helicase; 3'-5' DNA helicase; 3'-5' PfDH; 5' to 3' DNA helicase; AvDH1; BACH1 helicase; BcMCM; BLM protein; BRCA1-associated C-terminal helicase; CeWRN-1; Dbp9p; DmRECQ5; DNA helicase 120; DNA helicase A; DNA helicase E; DNA helicase II; DNA helicase III; DNA helicase RECQL5β; DNA helicase VI; dnaB; DnaB helicase E1; helicase HDH IV; Hel E; helicase DnaB; helicase domain of bacteriophage T7 gene 4 protein helicase; PcrA helicase; UvrD; hHcsA; Hmi1p; hPif1; MCM helicase; MCM protein; MER3 helicase; MER3 protein; MPH1; PcrA; PcrA helicase; PDH120; PfDH A; Pfh1p; PIF1

Systematic name: ATP phosphohydrolase (DNA helix unwinding)

Comments: DNA helicases utilize the energy from ATP hydrolysis to unwind double-stranded DNA. Some of them unwind duplex DNA with a 3' to 5' polarity [1,3,5,8], others show 5' to 3' polarity [10,11,12,13] or unwind DNA in both directions [14,15]. Some helicases unwind DNA as well as RNA [9,10]. May be identical with EC 3.6.4.13 (RNA helicase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Ozsoy, A.Z., Sekelsky, J.J. and Matson, S.W. Biochemical characterization of the small isoform of Drosophila melanogaster RECQ5 helicase. Nucleic Acids Res. 29 (2001) 2986-2993. [PMID: 11452023]

2. Tanner, J.A., Watt, R.M., Chai, Y.B., Lu, L.Y., Lin, M.C., Peiris, J.S., Poon, L.L., Kung, H.F. and Huang, J.D. The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5' to 3' viral helicases. J. Biol. Chem. 278 (2003) 39578-39582. [PMID: 12917423]

3. Nakagawa, T., Flores-Rozas, H. and Kolodner, R.D. The MER3 helicase involved in meiotic crossing over is stimulated by single-stranded DNA-binding proteins and unwinds DNA in the 3' to 5' direction. J. Biol. Chem. 276 (2001) 31487-31493. [PMID: 11376001]

4. Lee, C. and Seo, Y.S. Isolation and characterization of a processive DNA helicase from the fission yeast Schizosaccharomyces pombe that translocates in a 5'-to-3' direction. Biochem. J. 334 (1998) 377-386. [PMID: 9716495]

5. Phan, T.N., Ehtesham, N.Z., Tuteja, R. and Tuteja, N. A novel nuclear DNA helicase with high specific activity from Pisum sativum catalytically translocates in the 3'→5' direction. Eur. J. Biochem. 270 (2003) 1735-1745. [PMID: 12694186]

6. Bernstein, D.A., Zittel, M.C. and Keck, J.L. High-resolution structure of the E. coli RecQ helicase catalytic core. EMBO J. 22 (2003) 4910-4921. [PMID: 14517231]

7. Pike, A.C., Shrestha, B., Popuri, V., Burgess-Brown, N., Muzzolini, L., Costantini, S., Vindigni, A. and Gileadi, O. Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proc. Natl. Acad. Sci. USA 106:1039 (2009). [PMID: 19151156]

8. Curti, E., Smerdon, S.J. and Davis, E.O. Characterization of the helicase activity and substrate specificity of Mycobacterium tuberculosis UvrD. J. Bacteriol. 189 (2007) 1542-1555. [PMID: 17158674]

9. Frick, D.N. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr. Issues Mol. Biol. 9 (2007) 1-20. [PMID: 17263143]

10. Ivanov, K.A. and Ziebuhr, J. Human coronavirus 229E nonstructural protein 13: characterization of duplex-unwinding, nucleoside triphosphatase, and RNA 5'-triphosphatase activities. J. Virol. 78 (2004) 7833-7838. [PMID: 15220459]

11. Ivessa, A.S., Zhou, J.Q., Schulz, V.P., Monson, E.K. and Zakian, V.A. Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev. 16 (2002) 1383-1396. [PMID: 12050116]

12. Zhou, J.Q., Qi, H., Schulz, V.P., Mateyak, M.K., Monson, E.K. and Zakian, V.A. Schizosaccharomyces pombe pfh1+ encodes an essential 5' to 3' DNA helicase that is a member of the PIF1 subfamily of DNA helicases. Mol. Biol. Cell 13 (2002) 2180-2191. [PMID: 12058079]

13. George, T., Wen, Q., Griffiths, R., Ganesh, A., Meuth, M. and Sanders, C.M. Human Pif1 helicase unwinds synthetic DNA structures resembling stalled DNA replication forks. Nucleic Acids Res. 37 (2009) 6491-6502. [PMID: 19700773]

14. Naqvi, A., Tinsley, E. and Khan, S.A. Purification and characterization of the PcrA helicase of Bacillus anthracis. J. Bacteriol. 185 (2003) 6633-6639. [PMID: 14594837]

15. Ruiz-Maso, J.A., Anand, S.P., Espinosa, M., Khan, S.A. and del Solar, G. Genetic and biochemical characterization of the Streptococcus pneumoniae PcrA helicase and its role in plasmid rolling circle replication. J. Bacteriol. 188 (2006) 7416-7425. [PMID: 16936036]

[EC 3.6.4.12 created 2009]

EC 3.6.4.13

Accepted name: RNA helicase

Reaction: ATP + H2O = ADP + phosphate

Other name(s): CSFV NS3 helicase; DBP2; DbpA; DDX17; DDX25; DDX3; DDX3X; DDX3Y; DDX4; DDX5; DEAD-box protein DED1; DEAD-box RNA helicase; DEAH-box protein 2; DEAH-box RNA helicase; DED1; Dex(H/D) RNA helicase; EhDEAD1; EhDEAD1 RNA helicase; eIF4A helicase; KOKV helicase; Mtr4p; nonstructural protein 3 helicase; NPH-II; RHA; RNA helicase A; RNA helicase DDX3; RNA helicase Hera; RNA-dependent ATPase; TGBp1 NTPase/helicase domain; VRH1; GRTH/DDX25

Systematic name: ATP phosphohydrolase (RNA helix unwinding)

Comments: RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity [3], other show 5' to 3' polarity [8]. Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Cordin, O., Tanner, N.K., Doere, M., Linder, P. and Banroques, J. The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J. 23 (2004) 2478-2487. [PMID: 15201868]

2. Rodamilans, B. and Montoya, G. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the DDX3 RNA helicase domain. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63 (2007) 283-286. [PMID: 17401195]

3. Lee, C.G. and Hurwitz, J. A new RNA helicase isolated from HeLa cells that catalytically translocates in the 3' to 5' direction. J. Biol. Chem. 267 (1992) 4398-4407. [PMID: 1537828]

4. Li, S.C., Chung, M.C. and Chen, C.S. Cloning and characterization of a DEAD box RNA helicase from the viable seedlings of aged mung bean. Plant Mol. Biol. 47 (2001) 761-770. [PMID: 11785937]

5. Wu, J., Bera, A.K., Kuhn, R.J. and Smith, J.L. Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. J. Virol. 79 (2005) 10268-10277. [PMID: 16051820]

6. Gross, C.H. and Shuman, S. The nucleoside triphosphatase and helicase activities of vaccinia virus NPH-II are essential for virus replication. J. Virol. 72 (1998) 4729-4736. [PMID: 9573237]

7. Frick, D.N. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr. Issues Mol. Biol. 9 (2007) 1-20. [PMID: 17263143]

[EC 3.6.4.13 created 2009]


Continued with EC 3.6.5
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