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 now EC 5.6.1.8
EC 3.6.4.2 now EC 5.6.1.2
EC 3.6.4.3 now EC 5.6.1.1
EC 3.6.4.4 now EC 5.6.1.3
EC 3.6.4.5 now EC 5.6.1.4
EC 3.6.4.6 vesicle-fusing ATPase
EC 3.6.4.7 peroxisome-assembly ATPase
EC 3.6.4.8 now EC 5.6.1.5
EC 3.6.4.9 now EC 5.6.1.7
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 Transferred entry: myosin ATPase. Now EC 5.6.1.8, myosin ATPase(EC 3.6.4.1 created 1984 as EC 3.6.1.32, transferred 2000 to EC 3.6.4.1, deleted 2018)]

[EC 3.6.4.2 Transferred entry: dynein ATPase. Now EC 5.6.1.2, dynein ATPase(EC 3.6.4.2 created 1984 as EC 3.6.1.33, transferred 2000 to EC 3.6.4.2, deleted 2018)]

[EC 3.6.4.4 Transferred entry: plus-end-directed kinesin ATPase. Now EC 5.6.1.3, plus-end-directed kinesin ATPase(EC 3.6.4.4 created 2000, deleted 2018)]

[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 Transferred entry: minus-end-directed kinesin ATPase. Now EC 5.6.1.4, minus-end-directed kinesin ATPase(EC 3.6.4.5 created 2000, deleted 2018)]

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 Transferred entry: proteasome ATPase. Now EC 5.6.1.5, proteasome ATPase(EC 3.6.4.8 created 2000, deleted 2018)]

[EC 3.6.4.9 Transferred entry: chaperonin ATPase. Now EC 5.6.1.7, chaperonin ATPase(EC 3.6.4.9 created 2000, deleted 2018)]

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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