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PMID: 16877706 Published · ppublish English Journal Article Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.

Protein science : a publication of the Protein Society ·Vol. 15 ·No. 8 ·2006-08-00 ·Pages 1815-28

Rotanova TV, Botos I, Melnikov EE, Rasulova F, Gustchina A, Maurizi MR, Wlodawer A

Abstract

ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA(+) superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure-function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA(+) domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases.

MeSH Terms
Adenosine Triphosphate/metabolism Archaeoglobus fulgidus/enzymology Binding Sites/genetics Consensus Sequence/genetics Escherichia coli Proteins/chemistry Models, Molecular Protease La/chemistry,metabolism Protein Structure, Quaternary Protein Structure, Tertiary
Chemicals
Escherichia coli Proteins Adenosine Triphosphate Lon protein, E coli Protease La
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Rotanova Tatyana V
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
Botos Istvan
Melnikov Edward E
Rasulova Fatima
Gustchina Alla
Maurizi Michael R
Wlodawer Alexander
References (96)
96 references, click to expand
  1. [Peptide hydrolases with catalytic dyad Ser-Lys. Similarity and distinctions of the active centers of ATP-dependent Lon proteases, LexA repressors, signal peptidases and C-terminal processing proteases].
    Vopr Med Khim. 2002 Nov-Dec;48(6):541-52 PMID: 12698553
  2. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine.
    Cell. 2003 Aug 22;114(4):511-20 PMID: 12941278
  3. Proteolysis in bacterial regulatory circuits.
    Annu Rev Cell Dev Biol. 2003;19:565-87 PMID: 14570582
  4. [Proteolysis coupled with ATP. Regulation of activity of proteolytic centers of Escherichia coli lon protease].
    Bioorg Khim. 2003 Sep-Oct;29(5):486-94 PMID: 14601403
  5. Crystal structure of ClpX molecular chaperone from Helicobacter pylori.
    J Biol Chem. 2003 Dec 12;278(50):50664-70 PMID: 14514695
  6. MEROPS: the peptidase database.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D160-4 PMID: 14681384
  7. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.
    J Biol Chem. 2004 Feb 27;279(9):8140-8 PMID: 14665623
  8. Evolutionary history and higher order classification of AAA+ ATPases.
    J Struct Biol. 2004 Apr-May;146(1-2):11-31 PMID: 15037234
  9. Crystal structure of the AAA+ alpha domain of E. coli Lon protease at 1.9A resolution.
    J Struct Biol. 2004 Apr-May;146(1-2):113-22 PMID: 15037242
  10. Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone.
    J Struct Biol. 2004 Apr-May;146(1-2):166-79 PMID: 15037248
  11. Correlation of an adenine-specific conformational change with the ATP-dependent peptidase activity of Escherichia coli Lon.
    Biochemistry. 2004 Jun 15;43(23):7432-42 PMID: 15182186
  12. Functional domains of Brevibacillus thermoruber lon protease for oligomerization and DNA binding: role of N-terminal and sensor and substrate discrimination domains.
    J Biol Chem. 2004 Aug 13;279(33):34903-12 PMID: 15181012
  13. Sculpting the proteome with AAA(+) proteases and disassembly machines.
    Cell. 2004 Oct 1;119(1):9-18 PMID: 15454077
  14. Multiple regulator gene control of the galactose operon in Escherichia coli K-12.
    J Bacteriol. 1972 Jun;110(3):1089-99 PMID: 4555404
  15. Serine proteases: structure and mechanism of catalysis.
    Annu Rev Biochem. 1977;46:331-58 PMID: 332063
  16. The product of the lon (capR) gene in Escherichia coli is the ATP-dependent protease, protease La.
    Proc Natl Acad Sci U S A. 1981 Aug;78(8):4931-5 PMID: 6458037
  17. Protease La from Escherichia coli hydrolyzes ATP and proteins in a linked fashion.
    Proc Natl Acad Sci U S A. 1982 Aug;79(16):4883-7 PMID: 6214787
  18. [Cloning, expression and structure of the functionally active shortened lon gene in Escherichia coli].
    Bioorg Khim. 1988 Mar;14(3):408-11 PMID: 3289547
  19. [Cloning, structure and expression of the full-size lon gene in Escherichia coli coding for ATP-dependent La-proteinase].
    Bioorg Khim. 1990 Jul;16(7):869-80 PMID: 2242054
  20. The three-dimensional structure of proteasomes from Thermoplasma acidophilum as determined by electron microscopy using random conical tilting.
    FEBS Lett. 1991 May 20;283(1):117-21 PMID: 2037064
  21. LonR9 carrying a single Glu614 to Lys mutation inhibits the ATP-dependent protease La (Lon) by forming mixed oligomeric complexes.
    Biochem Biophys Res Commun. 1998 Sep 8;250(1):32-5 PMID: 9735326
  22. The role of the ClpA chaperone in proteolysis by ClpAP.
    Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12135-40 PMID: 9770452
  23. Catalytic triads and their relatives.
    Trends Biochem Sci. 1998 Sep;23(9):347-52 PMID: 9787641
  24. At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease.
    J Struct Biol. 1998 Nov;123(3):248-59 PMID: 9878579
  25. The sizes of peptides generated from protein by mammalian 26 and 20 S proteasomes. Implications for understanding the degradative mechanism and antigen presentation.
    J Biol Chem. 1999 Feb 5;274(6):3363-71 PMID: 9920878
  26. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.
    Genome Res. 1999 Jan;9(1):27-43 PMID: 9927482
  27. A conserved domain in Escherichia coli Lon protease is involved in substrate discriminator activity.
    J Bacteriol. 1999 Apr;181(7):2236-43 PMID: 10094703
  28. Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits.
    Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6787-90 PMID: 10359790
  29. Nucleotide dependent motion and mechanism of action of p97/VCP.
    J Mol Biol. 2005 Mar 25;347(2):437-52 PMID: 15740751
  30. Cleavage site selection within a folded substrate by the ATP-dependent lon protease.
    J Biol Chem. 2005 Jul 1;280(26):25103-10 PMID: 15870080
  31. Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases.
    J Mol Biol. 2005 Aug 5;351(1):144-57 PMID: 16002085
  32. Dysregulation of bacterial proteolytic machinery by a new class of antibiotics.
    Nat Med. 2005 Oct;11(10):1082-7 PMID: 16200071
  33. Structure of 20S proteasome from yeast at 2.4 A resolution.
    Nature. 1997 Apr 3;386(6624):463-71 PMID: 9087403
  34. Crystal structure of heat shock locus V (HslV) from Escherichia coli.
    Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6070-4 PMID: 9177170
  35. The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis.
    Cell. 1997 Nov 14;91(4):447-56 PMID: 9390554
  36. The lon protease from Mycobacterium smegmatis: molecular cloning, sequence analysis, functional expression, and enzymatic characterization.
    Biochemistry. 1998 Jan 6;37(1):377-86 PMID: 9425059
  37. The proteasome: paradigm of a self-compartmentalizing protease.
    Cell. 1998 Feb 6;92(3):367-80 PMID: 9476896
  38. Mutations in the proteolytic domain of Escherichia coli protease Lon impair the ATPase activity of the enzyme.
    FEBS Lett. 1998 Jan 30;422(2):218-20 PMID: 9490010
  39. [Synthesis and characterisation of ATP-dependent forms of Lon-proteinase with modified N-terminal domain from Escherichia coli].
    Bioorg Khim. 1998 May;24(5):370-5 PMID: 9661791
  40. Global unfolding of a substrate protein by the Hsp100 chaperone ClpA.
    Nature. 1999 Sep 2;401(6748):90-3 PMID: 10485712
  41. Nucleotide-dependent domain motions within rings of the RecA/AAA(+) superfamily.
    J Struct Biol. 2004 Dec;148(3):259-67 PMID: 15522774
  42. Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP.
    J Struct Biol. 2004 Dec;148(3):338-52 PMID: 15522782
  43. The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases.
    J Biol Chem. 2004 Dec 17;279(51):53451-7 PMID: 15456757
  44. Classification of ATP-dependent proteases Lon and comparison of the active sites of their proteolytic domains.
    Eur J Biochem. 2004 Dec;271(23-24):4865-71 PMID: 15606774
  45. Monitoring the timing of ATP hydrolysis with activation of peptide cleavage in Escherichia coli Lon by transient kinetics.
    Biochemistry. 2005 Feb 8;44(5):1671-82 PMID: 15683251
  46. Molecular machines for protein degradation.
    Chembiochem. 2005 Feb;6(2):222-56 PMID: 15678420
  47. Control of peptide product sizes by the energy-dependent protease ClpAP.
    Biochemistry. 2005 Oct 25;44(42):13921-31 PMID: 16229481
  48. Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines.
    Nature. 2005 Oct 20;437(7062):1115-20 PMID: 16237435
  49. Crystal structure of the N-terminal domain of E. coli Lon protease.
    Protein Sci. 2005 Nov;14(11):2895-900 PMID: 16199667
  50. Structural properties of substrate proteins determine their proteolysis by the mitochondrial AAA+ protease Pim1.
    Biol Chem. 2005 Dec;386(12):1307-17 PMID: 16336126
  51. Cleavage mechanism of ATP-dependent Lon protease toward ribosomal S2 protein.
    FEBS Lett. 2005 Dec 19;579(30):6846-50 PMID: 16337203
  52. The asymmetry in the mature amino-terminus of ClpP facilitates a local symmetry match in ClpAP and ClpXP complexes.
    J Struct Biol. 2006 Feb;153(2):113-28 PMID: 16406682
  53. Oligomeric structure of the ATP-dependent protease La (Lon) of Escherichia coli.
    Mol Cells. 2006 Feb 28;21(1):129-34 PMID: 16511355
  54. Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism.
    J Mol Biol. 2006 May 19;358(5):1378-89 PMID: 16584747
  55. Posttranslational quality control: folding, refolding, and degrading proteins.
    Science. 1999 Dec 3;286(5446):1888-93 PMID: 10583944
  56. The structures of HsIU and the ATP-dependent protease HsIU-HsIV.
    Nature. 2000 Feb 17;403(6771):800-5 PMID: 10693812
  57. AAA proteases: cellular machines for degrading membrane proteins.
    Trends Biochem Sci. 2000 May;25(5):247-51 PMID: 10782097
  58. Dynamics of substrate denaturation and translocation by the ClpXP degradation machine.
    Mol Cell. 2000 Apr;5(4):639-48 PMID: 10882100
  59. Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding.
    Cell. 2000 Jun 23;101(7):801-11 PMID: 10892750
  60. Site-directed mutagenesis of La protease. A catalytically active serine residue.
    FEBS Lett. 1991 Aug 5;287(1-2):211-4 PMID: 1652461
  61. The mechanism and functions of ATP-dependent proteases in bacterial and animal cells.
    Eur J Biochem. 1992 Jan 15;203(1-2):9-23 PMID: 1730246
  62. Regulation by proteolysis: energy-dependent proteases and their targets.
    Microbiol Rev. 1992 Dec;56(4):592-621 PMID: 1480111
  63. PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae.
    J Biol Chem. 1994 Jan 7;269(1):238-42 PMID: 8276800
  64. ATP-dependent protease La (lon) from Escherichia coli.
    Methods Enzymol. 1994;244:350-75 PMID: 7845219
  65. Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution.
    Science. 1995 Apr 28;268(5210):533-9 PMID: 7725097
  66. Structure of the UmuD' protein and its regulation in response to DNA damage.
    Nature. 1996 Apr 25;380(6576):727-30 PMID: 8614470
  67. Proteases and their targets in Escherichia coli.
    Annu Rev Genet. 1996;30:465-506 PMID: 8982462
  68. Functional role of the N-terminal region of the Lon protease from Mycobacterium smegmatis.
    Biochemistry. 1998 Aug 11;37(32):11255-63 PMID: 9698372
  69. The isolated proteolytic domain of Escherichia coli ATP-dependent protease Lon exhibits the peptidase activity.
    FEBS Lett. 1998 Aug 7;432(3):179-81 PMID: 9720920
  70. The ATPase and protease domains of yeast mitochondrial Lon: roles in proteolysis and respiration-dependent growth.
    Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10584-9 PMID: 9724747
  71. Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein.
    Cell. 1998 Aug 21;94(4):525-36 PMID: 9727495
  72. Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP.
    Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8898-903 PMID: 10922052
  73. A gated channel into the proteasome core particle.
    Nat Struct Biol. 2000 Nov;7(11):1062-7 PMID: 11062564
  74. Structural basis for the activation of 20S proteasomes by 11S regulators.
    Nature. 2000 Nov 2;408(6808):115-20 PMID: 11081519
  75. Crystal and solution structures of an HslUV protease-chaperone complex.
    Cell. 2000 Nov 10;103(4):633-43 PMID: 11106733
  76. The rotary mechanism of ATP synthase.
    Curr Opin Struct Biol. 2000 Dec;10(6):672-9 PMID: 11114504
  77. Structure of the AAA ATPase p97.
    Mol Cell. 2000 Dec;6(6):1473-84 PMID: 11163219
  78. ClpA mediates directional translocation of substrate proteins into the ClpP protease.
    Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3768-72 PMID: 11259663
  79. [Coupling of proteolysis and hydrolysis of ATP upon functioning of Lon proteinase of Escherichia coli. II. Hydrolysis of ATP and activity of peptide hydrolase sites of the enzyme].
    Bioorg Khim. 2001 Mar-Apr;27(2):120-9 PMID: 11357396
  80. Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine.
    EMBO J. 2001 Jun 15;20(12):3092-100 PMID: 11406586
  81. Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
    Structure. 2001 Feb 7;9(2):177-84 PMID: 11250202
  82. AAA+ superfamily ATPases: common structure--diverse function.
    Genes Cells. 2001 Jul;6(7):575-97 PMID: 11473577
  83. Mg2+-linked oligomerization modulates the catalytic activity of the Lon (La) protease from Mycobacterium smegmatis.
    Biochemistry. 2001 Aug 7;40(31):9317-23 PMID: 11478899
  84. Crystal structure of LexA: a conformational switch for regulation of self-cleavage.
    Cell. 2001 Sep 7;106(5):585-94 PMID: 11551506
  85. AAA proteins: in search of a common molecular basis. International Meeting on Cellular Functions of AAA Proteins.
    EMBO Rep. 2001 Nov;2(11):980-5 PMID: 11713188
  86. Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site.
    Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1950-4 PMID: 11717526
  87. Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism.
    J Biol Chem. 2002 Mar 15;277(11):9512-9 PMID: 11741964
  88. The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase.
    J Biol Chem. 2002 Jul 19;277(29):25976-82 PMID: 12011053
  89. The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution.
    Structure. 2002 Aug;10(8):1073-83 PMID: 12176385
  90. Lon protease preferentially degrades oxidized mitochondrial aconitase by an ATP-stimulated mechanism.
    Nat Cell Biol. 2002 Sep;4(9):674-80 PMID: 12198491
  91. Domain structure and ATP-induced conformational changes in Escherichia coli protease Lon revealed by limited proteolysis and autolysis.
    FEBS Lett. 2002 Aug 28;526(1-3):66-70 PMID: 12208506
  92. Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8.
    Structure. 2002 Oct;10(10):1415-23 PMID: 12377127
  93. Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease.
    J Biol Chem. 2002 Nov 29;277(48):46743-52 PMID: 12205096
  94. Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle.
    Nat Struct Biol. 2002 Dec;9(12):950-7 PMID: 12434150
  95. AAA proteins.
    Curr Opin Struct Biol. 2002 Dec;12(6):746-53 PMID: 12504679
  96. [Catalytic dyad Ser-Lys at the active site of Escherichia coli ATP-dependent Lon-proteinase].
    Bioorg Khim. 2003 Jan-Feb;29(1):97-9 PMID: 12658998
Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
DOI
10.1110/ps.052069306
Published
2006-08-00
Pages
1815-28
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2242575
Subset
IM
Grants
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1110/ps.052069306 PMC Full Text View journal details
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