User:Amy Rumora/Sandbox 1
From Proteopedia
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===The structure of BACE1 catalytic core=== | ===The structure of BACE1 catalytic core=== | ||
{{STRUCTURE_1fkn| PDB=1fkn | SCENE= }} | {{STRUCTURE_1fkn| PDB=1fkn | SCENE= }} | ||
| - | BACE1 is a bilobal protein that consists of luminal N-lobe and C-lobe anchored to the plasma membrane by a transmembrane domain that exposes a small cytosolic domain. The catalytic core of BACE1, shown here, spans amino acid residues 43-385. BACE1 is a member of the mainly beta class of proteins with a β-barrel architecture. This structure is composed of <scene name='User:Amy_Rumora/Sandbox_1/2zht_2ndary/1'>12 helices and 28 sheets</scene> (shown in green and grey, respectively). Unlike other class I aspartic proteases, insertions and an extension in the C-terminus of BACE1 creates an enlarged C-terminal lobe. <scene name='User:Amy_Rumora/Sandbox_1/Acdf/1'>Insertion helix A and insertion loops C, D, and F</scene> are localized on the surface of the C-lobe adjacent from the N-terminus of bound inhibitors. Four acidic amino acid residues on the F insertion loop form a negatively charged area on the surface of the enzyme. <scene name='User:Amy_Rumora/Sandbox_1/Acdfbe/1'>Insertion loops B and E</scene> are located on the surface of the C-lobe near the C-terminus of bound inhibitors. These BACE1 insertions may | + | BACE1 is a bilobal protein that consists of luminal N-lobe and C-lobe anchored to the plasma membrane by a transmembrane domain that exposes a small cytosolic domain. The catalytic core of BACE1, shown here, spans amino acid residues 43-385. BACE1 is a member of the mainly beta class of proteins with a β-barrel architecture. This structure is composed of <scene name='User:Amy_Rumora/Sandbox_1/2zht_2ndary/1'>12 helices and 28 sheets</scene> (shown in green and grey, respectively). Unlike other class I aspartic proteases, insertions and an extension in the C-terminus of BACE1 creates an enlarged C-terminal lobe. <scene name='User:Amy_Rumora/Sandbox_1/Acdf/1'>Insertion helix A and insertion loops C, D, and F</scene> are localized on the surface of the C-lobe adjacent from the N-terminus of bound inhibitors. Four acidic amino acid residues on the F insertion loop form a negatively charged area on the surface of the enzyme. <scene name='User:Amy_Rumora/Sandbox_1/Acdfbe/1'>Insertion loops B and E</scene> are located on the surface of the C-lobe near the C-terminus of bound inhibitors. These BACE1 insertions may form interactions with cell surface components and enlarge the C-terminal surface area to make the active site more accessible to substrates<ref>PMID:11021803</ref>. A 35 residue C-terminal <scene name='User:Amy_Rumora/Sandbox_1/Extension/1'>extension</scene> (359-385) forms an ordered β structure spanning residues 369-376 and a helix between residues 378-383. This structure may form a stem with the transmembrane domain. BACE1 contains three structural disulfide bonds. The positioning of these disulfide bonds within BACE1 varies greatly from the location of disulfide bonds in other Class I aspartic proteases<ref>PMID:10749877</ref>. The three structural disulfide bonds maintain the correct fold of BACE1 but are not involved in BACE1 catalysis<ref>PMID:10887202</ref><ref>PMID:11953458</ref>. |
===Structural elements involved in catalysis=== | ===Structural elements involved in catalysis=== | ||
Revision as of 16:26, 23 April 2009
Contents |
BACE1
BACE1 (β-site of APP cleaving enzyme) also called β-Secretase and memapsin-2 is a 52 kD class I transmembrane aspartic acid protease that cleaves the Amyloid Precursor Protein (APP) in a rate limiting step that contributes to the accumulation of β-amyloid plaques in Alzheimer’s disease (AD). A subsequent cleavage by γ-secretase generates a 40 or 42 amino acid β-amyloid peptide. These peptides can form Aβ plaques that may have deleterious effects on neuronal function and contribute to pathologies of AD. Under normal conditions, BACE1 activity generates a monomeric and soluble Aβ peptide that may play a physiological role in decreasing excitotoxicity and neurotransmission at glutamatergic synapses. Additionally, α-secretase and γ-secretase cleave APP to generate p3 and the carboxy terminal fragment AICD in a non-amyloidogenic pathway. In AD, amyloidogenic pathways become preferential over non-amyloidogenic and Aβ plaques appear under increased levels of BACE1 catalytic activity.
The structure of BACE1 catalytic core
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| 1fkn, resolution 1.90Å () | |||||||||
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| Non-Standard Residues: | |||||||||
| Activity: | Memapsin 2, with EC number 3.4.23.46 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
BACE1 is a bilobal protein that consists of luminal N-lobe and C-lobe anchored to the plasma membrane by a transmembrane domain that exposes a small cytosolic domain. The catalytic core of BACE1, shown here, spans amino acid residues 43-385. BACE1 is a member of the mainly beta class of proteins with a β-barrel architecture. This structure is composed of (shown in green and grey, respectively). Unlike other class I aspartic proteases, insertions and an extension in the C-terminus of BACE1 creates an enlarged C-terminal lobe. are localized on the surface of the C-lobe adjacent from the N-terminus of bound inhibitors. Four acidic amino acid residues on the F insertion loop form a negatively charged area on the surface of the enzyme. are located on the surface of the C-lobe near the C-terminus of bound inhibitors. These BACE1 insertions may form interactions with cell surface components and enlarge the C-terminal surface area to make the active site more accessible to substrates[1]. A 35 residue C-terminal (359-385) forms an ordered β structure spanning residues 369-376 and a helix between residues 378-383. This structure may form a stem with the transmembrane domain. BACE1 contains three structural disulfide bonds. The positioning of these disulfide bonds within BACE1 varies greatly from the location of disulfide bonds in other Class I aspartic proteases[2]. The three structural disulfide bonds maintain the correct fold of BACE1 but are not involved in BACE1 catalysis[3][4].
Structural elements involved in catalysis
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| 1w50, resolution 1.75Å () | |||||||||
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| Ligands: | |||||||||
| Activity: | Memapsin 2, with EC number 3.4.23.46 | ||||||||
| Related: | 1fkn, 1m4h, 1py1, 1sgz, 1ujj, 1ujk, 1w51 | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
An aspartic acid dyad is located in the active site between the N- and C- terminal lobes. Active site are in a coplanar configuration that allows them to coordinate and activate a water molecule. The activated water performs a nucleophilic attack on the peptide carbonyl group of the substrate. Hydrogen bonds between the carbonyl group of the aspartates and the substrate stabilize a geminal diol intermediate. A proton is then transferred from aspartate to the leaving group resulting in peptide bond breakage between Met671 and Asp672 of APP. The products of the hydrolysis reaction leave the active site[5]. The active site of BACE1 is covered by a 10 amino acid flexible antiparallel β-hairpin called the . This flap controls the entrance of substrates into the active site and is in closed conformation in the presence of bound inhibitors and open conformation in the inactive or apo structures. A Cα of 7Å is visible in the inhibitor bound BACE1 complex in comparison to the apo structure[6]. Tyrosine 71 is a conserved residue located at the tip of the flap that undergoes large conformational changes. In apo BACE1 structures, Tyr71 forms a hydrogen bond allowing the flap to adopt a more open conformation. In the presence of inhibitor, the phenolic ring of Tyr71 forms a weak hydrogen bond with Tryptophan 76 causing the flap to adopt a closed conformation. Additionally, the 10s loop undergoes conformational change in the presence of an inhibitor. This loop may confer specificity for the correct substrate.
Image:Asparticmech.png http://en.wikipedia.org
BACE1 as a therapeutic target for AD
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| 2zhr, resolution 2.50Å () | |||||||||
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| Non-Standard Residues: | |||||||||
| Gene: | BACE1 (Homo sapiens) | ||||||||
| Activity: | Memapsin 2, with EC number 3.4.23.46 | ||||||||
| Related: | 2zhs, 2zht, 2zhu, 2zhv | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
BACE1 is a major therapeutic target due it's role in generating Aβ plaques that contribute to AD pathogenesis. There are currently over 70 structures of BACE1 complexed with inhibitors in the protein data bank http://www.rcsb.org/. These studies have not only developed inhibitors that efficiently block BACE1 activity, but also provide a greater understanding of the residues and regions that interact with the substrate in the active site of BACE1. The first inhibitor crystallized in complex with BACE1 was OM99-2. is a transition state analogue inhibitor that is eight residues in length (Glu-Val-Asn-Leu*-Ala-Ala-Glu-Phe) designated P4-P4’ (P4-P3-P2-P1*-P1’-P2’-P3’-P4’). OM99-2 inhibits BACE1 cleavage between the P1*-P1’ bond because of the presence of a hydroxyethylene isotere (*) that cannot be cleaved. The S1 and S3 sites that bind P1 and P3 are hydrophobic pockets that bind uncharged residues of the substrate [7]. On the other hand, sites S2 and S4 contain hydrophilic residues such as Arg that accommodate charged residues [8][9]. Sites S5-S7 are in the proximity of the insertion helix and may be important for recognition of the substrate [10]. The maintains a closed conformation over OM99-2 through hydrogen bonding between the conserved Tyr71 residue and the substrate at positions P1 and P2' [11][12]. Additionally, a conformational displacement is observed for the in the hydrophobic S3 site of the BACE1 active site upon binding of an inhibitor.
Evolutionary conservation in the asparic protease family
Members of the aspartic protease family have structural features that are evolutionarily conserved and appear in most aspartic proteases. Pepsin, Cathepsin D, Chymosin, and renin are members of the aspartic protease family and are evolutionarily related to BACE1. Like BACE1, these proteins have a bilobal structure, a catalytic dyad composed of two Asp, and have a β-barrel architecture. On the other hand, BACE1 has several unique features that separate it from other aspartic proteases. Currently, BACE1 is the only member of this family that is a transmembrane protein. The addition of extension loops and helices enlarge the BACE1 C-lobe and the location of disulfide bonds varies in comparison to other aspartic proteases.
Links
- 1w50 (Apo structure of bace (beta secretase))
- 1w51 (Bace (beta secretase) in complex with a nanomolar non-peptidic inhibitor)
- 2zhs, 2zht, 2zhu, 2zhv (Crystal structure of BACE1 at varying pH)
- 2zhr (Crystal structure of BACE1 in complex with OM99-2 at pH 5.0)
- 1fkn (Structure of Beta-Secretase Complexed with Inhibitor)
References
- ↑ Hong L, Koelsch G, Lin X, Wu S, Terzyan S, Ghosh AK, Zhang XC, Tang J. Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. Science. 2000 Oct 6;290(5489):150-3. PMID:11021803
- ↑ Bennett BD, Babu-Khan S, Loeloff R, Louis JC, Curran E, Citron M, Vassar R. Expression analysis of BACE2 in brain and peripheral tissues. J Biol Chem. 2000 Jul 7;275(27):20647-51. PMID:10749877 doi:10.1074/jbc.M002688200
- ↑ Haniu M, Denis P, Young Y, Mendiaz EA, Fuller J, Hui JO, Bennett BD, Kahn S, Ross S, Burgess T, Katta V, Rogers G, Vassar R, Citron M. Characterization of Alzheimer's beta -secretase protein BACE. A pepsin family member with unusual properties. J Biol Chem. 2000 Jul 14;275(28):21099-106. PMID:10887202 doi:10.1074/jbc.M002095200
- ↑ Fischer F, Molinari M, Bodendorf U, Paganetti P. The disulphide bonds in the catalytic domain of BACE are critical but not essential for amyloid precursor protein processing activity. J Neurochem. 2002 Mar;80(6):1079-88. PMID:11953458
- ↑ Shimizu H, Tosaki A, Kaneko K, Hisano T, Sakurai T, Nukina N. Crystal structure of an active form of BACE1, an enzyme responsible for amyloid beta protein production. Mol Cell Biol. 2008 Jun;28(11):3663-71. Epub 2008 Mar 31. PMID:18378702 doi:10.1128/MCB.02185-07
- ↑ Patel S, Vuillard L, Cleasby A, Murray CW, Yon J. Apo and inhibitor complex structures of BACE (beta-secretase). J Mol Biol. 2004 Oct 15;343(2):407-16. PMID:15451669 doi:10.1016/j.jmb.2004.08.018
- ↑ Stockley JH, O'Neill C. Understanding BACE1: essential protease for amyloid-beta production in Alzheimer's disease. Cell Mol Life Sci. 2008 Oct;65(20):3265-89. PMID:18695942 doi:10.1007/s00018-008-8271-3
- ↑ Ostermann N, Eder J, Eidhoff U, Zink F, Hassiepen U, Worpenberg S, Maibaum J, Simic O, Hommel U, Gerhartz B. Crystal structure of human BACE2 in complex with a hydroxyethylamine transition-state inhibitor. J Mol Biol. 2006 Jan 13;355(2):249-61. Epub 2005 Nov 8. PMID:16305800 doi:10.1016/j.jmb.2005.10.027
- ↑ Hong L, Koelsch G, Lin X, Wu S, Terzyan S, Ghosh AK, Zhang XC, Tang J. Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. Science. 2000 Oct 6;290(5489):150-3. PMID:11021803
- ↑ Turner RT 3rd, Hong L, Koelsch G, Ghosh AK, Tang J. Structural locations and functional roles of new subsites S5, S6, and S7 in memapsin 2 (beta-secretase). Biochemistry. 2005 Jan 11;44(1):105-12. PMID:15628850 doi:10.1021/bi048106k
- ↑ Hong L, Tang J. Flap position of free memapsin 2 (beta-secretase), a model for flap opening in aspartic protease catalysis. Biochemistry. 2004 Apr 27;43(16):4689-95. PMID:15096037 doi:10.1021/bi0498252
- ↑ Shimizu H, Tosaki A, Kaneko K, Hisano T, Sakurai T, Nukina N. Crystal structure of an active form of BACE1, an enzyme responsible for amyloid beta protein production. Mol Cell Biol. 2008 Jun;28(11):3663-71. Epub 2008 Mar 31. PMID:18378702 doi:10.1128/MCB.02185-07
