Structure-Based Dissection of the Active Site Chemistry of Leukotriene A4 Hydrolase: Implications for M1 Aminopeptidases and Inhibitor Design

Tholander, Fredrik; Muroya, A.; Roques, B. P.; Fournié‐Zaluski, Marie‐Claude; Thunnissen, Marjolein M.G.M.; Haeggström, Jesper Z.

doi:10.1016/j.chembiol.2008.07.018

Cited by 84 publications

(105 citation statements)

References 45 publications

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“…1). The overall four-domain architecture of ERAP1 is remarkably similar to previously solved structures of Tricorn interacting factor F3 (PDB ID code 1Z5H) (19), aminopeptidase N from Escherichia coli (ePepN, PDB ID code 2ZXG) (20,21), and Leukotriene A4 hydrolase/aminopeptidase (LTA4H, PDB ID codes 1HS6 and 3B7U) (22,23), the latter being the closest structurally characterized eukaryotic ortholog (39% overall homology) that does not contain Domain III ( Fig. S2; for comparison of domain similarities cf.…”

Section: Resultsmentioning

confidence: 55%

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming

Kochan

Krojer

Harvey

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

235

286

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Endoplasmatic reticulum aminopeptidase 1 (ERAP1) is a multifunctional enzyme involved in trimming of peptides to an optimal length for presentation by major histocompatibility complex (MHC) class I molecules. Polymorphisms in ERAP1 have been associated with chronic inflammatory diseases, including ankylosing spondylitis (AS) and psoriasis, and subsequent in vitro enzyme studies suggest distinct catalytic properties of ERAP1 variants. To understand structure-activity relationships of this enzyme we determined crystal structures in open and closed states of human ERAP1, which provide the first snapshots along a catalytic path. ERAP1 is a zinc-metallopeptidase with typical H-E-X-X-H-ðXÞ 18 -E zinc binding and G-A-M-E-N motifs characteristic for members of the gluzincin protease family. The structures reveal extensive domain movements, including an active site closure as well as three different open conformations, thus providing insights into the catalytic cycle. A K 528 R mutant strongly associated with AS in GWAS studies shows significantly altered peptide processing characteristics, which are possibly related to impaired interdomain interactions.antigen presentation | ERAP1 mechanism | MHC restriction

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Section: Resultsmentioning

confidence: 55%

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming

Kochan

Krojer

Harvey

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

235

286

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“…Another structurally characterized gluzincin family consists of leukotriene A4 hydrolase (PDB 3B7S (87)) and related metalloaminopeptidases such as cold-active aminopeptidase (PDB 3CIA (88)), endoplasmic reticulum aminopeptidase 1 (PDB 3QNF and 3MDJ (89,90)), tricorn interacting factor F3 (PDB 1Z5H (91)), M1 alanyl aminopeptidase (PDB 3EBI (92)), and aminopeptidase N (PDB 2HPO (93)). Like cowrins (82), these are large multidomain enzymes spanning ϳ600 -950 residues that contain an inserted CD bearing a greater resemblance to proabylysin and projannalysin than that of thermolysin (DALI Z values between 7.2 and 6.4).…”

Section: Resultsmentioning

confidence: 99%

A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

López-Pelegrín

Cerdà-Costa

Martínez-Jiménez

et al. 2013

Journal of Biological Chemistry

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Background: Structural characterization of integral-membrane (IM) metallopeptidases (MPs) faces enormous technical hurdles. Results:We have discovered a novel family of minimal MPs, minigluzincins, and determined the crystal structures of the zymogens of two family members. Conclusion:Minigluzincins are valid models for catalytic domains of M48 and M56 family IMMPs. Significance: They provide a high resolution scaffold for the design of small molecule inhibitors of IMMPs.

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“…The basic amino acids Arg and L-homoarginine are also among the preferred amino acids. This is not surprising given recent structural analysis of leukotriene A4 hydrolase/aminopeptidase, which belongs to the same family as APN (32). Leukotriene A4 hydrolase (LTA4H) almost equally processed Ala and Arg substrates coupled to the p-nitroanilide chromophore.…”

Section: H Nmr and Lc-ms)mentioning

confidence: 99%

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

Drąg

Bogyo

Ellman

et al. 2010

Journal of Biological Chemistry

119

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Aminopeptidases process the N-terminal amino acids of target substrates by sequential cleavage of one residue at a time. They are found in all cell compartments of prokaryotes and eukaryotes, being implicated in the major proteolytic events of cell survival, defense, growth, and development. We present a new approach for the fast and reliable evaluation of the substrate specificity of individual aminopeptidases. Using solid phase chemistry with the 7-amino-4-carbamoylmethylcoumarin fluorophore, we have synthesized a library of 61 individual natural and unnatural amino acids substrates, chosen to cover a broad spectrum of the possible interactions in the S1 pocket of this type of protease. As proof of concept, we determined the substrate specificity of human, pig, and rat orthologs of aminopeptidase N (CD13), a highly conserved cell surface protease that inactivates enkephalins and other bioactive peptides. Our data reveal a large and hydrophobic character for the S1 pocket of aminopeptidase N that is conserved with aminopeptidase Ns. Our approach, which can be applied in principle to all aminopeptidases, yields useful information for the design of specific inhibitors, and more importantly, reveals a relationship between the kinetics of substrate hydrolysis and the kinetics of enzyme inhibition.The largest group of aminopeptidases, proteases that remove amino acids from the N terminus of target substrates one residue at a time, are members of the metallopeptidases (1). They are found in most cell compartments of prokaryotes and eukaryotes and are implicated in several major cell fates such as maintenance of the differentiated state, defense against pathogens, growth, and development (2-4). A classic aminopeptidase activity is the removal of the N-terminal Met after the initiation of translation by methionine aminopeptidase (5, 6). In addition to their primary proteolytic function, aminopeptidases also play secondary roles as viral or toxin receptors, transcriptional repressors, and vesicular trafficking controllers (7-9). The activity of well known aminopeptidases and the characterization of new aminopeptidases are generally determined using synthetic substrates containing one of a few natural amino acids attached to chromogenic or fluorogenic leaving groups (10, 11). For example, the M1 clan (alanine aminopeptidases) is assayed using fluorogenic peptide substrates containing a P1 Ala, and the M17 clan (leucine aminopeptidases) is assayed using fluorogenic peptide substrates containing a P1 Leu (12-14). However, this type of evaluation of enzyme specificity gives limited information about the profile of the S1 pocket, a primary determinant in the absolute specificity of aminopeptidases for their natural substrates.A number of general substrate-based library screening methods have been developed for the fast and reliable determination of protease specificity (15)(16)(17)(18)(19)(20). Importantly, for the cysteine, serine, and threonine proteases, substrate specificity data provide valuable information that can be ...

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Structure-Based Dissection of the Active Site Chemistry of Leukotriene A4 Hydrolase: Implications for M1 Aminopeptidases and Inhibitor Design

Cited by 84 publications

References 45 publications

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming

A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

Aminopeptidase Fingerprints, an Integrated Approach for Identification of Good Substrates and Optimal Inhibitors

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