Amidation of Bioactive Peptides: the Structure of the Lyase Domain of the Amidating Enzyme

Overview

Journal Structure

Publisher Cell Press

Specialties Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Date 2009 Jul 17

PMID 19604476

Citations 43

Authors

Eduardo E Chufan

Mithu De

Betty A Eipper

Richard E Mains

L Mario Amzel

Affiliations

Soon will be listed here.

Abstract

Many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. The enzyme peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL; EC 4.3.2.5) catalyzes the second and last step of this reaction, N-dealkylation of the peptidyl-alpha-hydroxyglycine to generate the alpha-amidated peptide and glyoxylate. Here we report the X-ray crystal structure of the PAL catalytic core (PALcc) alone and in complex with the nonpeptidic substrate alpha-hydroxyhippuric acid. The structures show that PAL folds as a six-bladed beta-propeller. The active site is formed by a Zn(II) ion coordinated by three histidine residues; the substrate binds to this site with its alpha-hydroxyl group coordinated to the Zn(II) ion. The structures also reveal a tyrosine residue (Tyr(654)) at the active site as the catalytic base for hydroxyl deprotonation, an unusual role for tyrosine. A reaction mechanism is proposed based on this structural data and validated by biochemical analysis of site-directed PALcc mutants.

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References

. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 5):760-3. DOI: 10.1107/S0907444994003112. View

Klinman J . The copper-enzyme family of dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase: resolving the chemical pathway for substrate hydroxylation. J Biol Chem. 2005; 281(6):3013-6. DOI: 10.1074/jbc.R500011200. View

Lang R, Kocourek A, Braun M, Tschesche H, Huber R, Bode W . Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure. J Mol Biol. 2001; 312(4):731-42. DOI: 10.1006/jmbi.2001.4954. View

Kent U, Fleming P . Purified cytochrome b561 catalyzes transmembrane electron transfer for dopamine beta-hydroxylase and peptidyl glycine alpha-amidating monooxygenase activities in reconstituted systems. J Biol Chem. 1987; 262(17):8174-8. View

Prigge S, Mains R, Eipper B, Amzel L . New insights into copper monooxygenases and peptide amidation: structure, mechanism and function. Cell Mol Life Sci. 2000; 57(8-9):1236-59. PMC: 11146793. DOI: 10.1007/pl00000763. View

Luo Y, Samuel J, Mosimann S, Lee J, Tanner M, Strynadka N . The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. Biochemistry. 2001; 40(49):14763-71. DOI: 10.1021/bi0112513. View

Toney J, Hammond G, Fitzgerald P, Sharma N, Balkovec J, Rouen G . Succinic acids as potent inhibitors of plasmid-borne IMP-1 metallo-beta-lactamase. J Biol Chem. 2001; 276(34):31913-8. DOI: 10.1074/jbc.M104742200. View

Jones T, Zou J, Cowan S, Kjeldgaard M . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991; 47 ( Pt 2):110-9. DOI: 10.1107/s0108767390010224. View

Maskos K, Huber R, Bourenkov G, Bartunik H, Ellestad G, Reddy P . Crystal structure of the catalytic domain of human tumor necrosis factor-alpha-converting enzyme. Proc Natl Acad Sci U S A. 1998; 95(7):3408-12. PMC: 19849. DOI: 10.1073/pnas.95.7.3408. View

10.

Prigge S, Kolhekar A, Eipper B, Mains R, Amzel L . Amidation of bioactive peptides: the structure of peptidylglycine alpha-hydroxylating monooxygenase. Science. 1997; 278(5341):1300-5. DOI: 10.1126/science.278.5341.1300. View

11.

Penning T, Bennett M, Schlegel B, Jez J, Lewis M . Structure and function of 3 alpha-hydroxysteroid dehydrogenase. Steroids. 1997; 62(1):101-11. DOI: 10.1016/s0039-128x(96)00167-5. View

12.

Kolhekar A, Roberts M, Jiang N, Johnson R, Mains R, Eipper B . Neuropeptide amidation in Drosophila: separate genes encode the two enzymes catalyzing amidation. J Neurosci. 1997; 17(4):1363-76. PMC: 6793724. View

13.

Crespo A, Marti M, Roitberg A, Amzel L, Estrin D . The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation. J Am Chem Soc. 2006; 128(39):12817-28. DOI: 10.1021/ja062876x. View

14.

Slack F, Ruvkun G . A novel repeat domain that is often associated with RING finger and B-box motifs. Trends Biochem Sci. 1998; 23(12):474-5. DOI: 10.1016/s0968-0004(98)01299-7. View

15.

Kolhekar A, Bell J, Shiozaki E, Jin L, Keutmann H, Hand T . Essential features of the catalytic core of peptidyl-alpha-hydroxyglycine alpha-amidating lyase. Biochemistry. 2002; 41(41):12384-94. DOI: 10.1021/bi0260280. View

16.

Krishnamurthy V, Kaufman G, Urbach A, Gitlin I, Gudiksen K, Weibel D . Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev. 2008; 108(3):946-1051. PMC: 2740730. DOI: 10.1021/cr050262p. View

17.

Prigge S, Eipper B, Mains R, Amzel L . Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex. Science. 2004; 304(5672):864-7. DOI: 10.1126/science.1094583. View

18.

Navaza J . Implementation of molecular replacement in AMoRe. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 10):1367-72. DOI: 10.1107/s0907444901012422. View

19.

Prigge S, Kolhekar A, Eipper B, Mains R, Amzel L . Substrate-mediated electron transfer in peptidylglycine alpha-hydroxylating monooxygenase. Nat Struct Biol. 1999; 6(10):976-83. DOI: 10.1038/13351. View

20.

Chen P, Solomon E . O2 activation by binuclear Cu sites: noncoupled versus exchange coupled reaction mechanisms. Proc Natl Acad Sci U S A. 2004; 101(36):13105-10. PMC: 516532. DOI: 10.1073/pnas.0402114101. View