4IJO

Unraveling hidden allosteric regulatory sites in structurally homologues metalloproteases

DOI: 10.2210/pdb4IJO/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-12-22 Released: 2013-05-01
Deposition Author(s): Udi, Y., Fragai, M., Grossman, M., Mitternacht, S., Arad-Yellin, R., Calderone, V., Melikian, M., Toccafondi, M., Berezovsky, I.N., Luchinat, C., Sagi, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.183
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Unraveling hidden regulatory sites in structurally homologous metalloproteases

Udi, Y., Fragai, M., Grossman, M., Mitternacht, S., Arad-Yellin, R., Calderone, V., Melikian, M., Toccafondi, M., Berezovsky, I.N., Luchinat, C., Sagi, I.

(2013) J Mol Biol 425: 2330-2346

PubMed: 23583775 Search on PubMed
DOI: 10.1016/j.jmb.2013.04.009
Primary Citation of Related Structures:
4IJO

PubMed Abstract:

Monitoring enzymatic activity in vivo of individual homologous enzymes such as the matrix metalloproteinases (MMPs) by antagonist molecules is highly desired for defining physiological and pathophysiological pathways. However, the rational design of antagonists targeting enzyme catalytic moieties specific to one of the homologous enzymes often appears to be an extremely difficult task. This is mainly due to the high structural homology at the enzyme active sites shared by members of the protein family. Accordingly, controlling enzymatic activity via alternative allosteric sites has become an attractive proposition for drug design targeting individual homologous enzymes. Yet, the challenge remains to identify such regulatory alternative sites that are often hidden and scattered over different locations on the protein's surface. We have designed branched amphiphilic molecules exhibiting specific inhibitory activity towards individual members of the MMP family. These amphiphilic isomers share the same chemical nature, providing versatile nonspecific binding reactivity that allows to probe hidden regulatory residues on a given protein surface. Using the advantage provided by amphiphilic ligands, here we explore a new approach for determining hidden regulatory sites. This approach includes diverse experimental analysis, such as structural spectroscopic analyses, NMR, and protein crystallography combined with computational prediction of effector binding sites. We demonstrate how our approach works by analyzing members of the MMP family that possess a unique set of such sites. Our work provides a proof of principle for using ligand effectors to unravel hidden regulatory sites specific to members of the structurally homologous MMP family. This approach may be exploited for the design of novel molecular effectors and therapeutic agents affecting protein catalytic function via interactions with structure-specific regulatory sites.

Related Citations:

Snapshots of the reaction mechanism of matrix metalloproteinases
Bertini, I., Calderone, V., Fragai, M., Luchinat, C., Maletta, M., Yeo, K.J.
(2006) Angew Chem Int Ed Engl 45(47): 7952

Conformational variability of matrix metalloproteinases: beyond a single 3D structure
Bertini, I., Calderone, V., Cosenza, M., Fragai, M., Lee, Y.M., Luchinat, C., Mangani, S., Terni, B., Turano, P.
(2005) Proc Natl Acad Sci U S A 102(15): 5334

Organizational Affiliation:

Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	158	Homo sapiens	Mutation(s): 1 Gene Names: MMP12, HME EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens) Explore P39900 Go to UniProtKB: P39900
NIH Common Fund Data Resources
PHAROS: P39900 GTEx: ENSG00000262406
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain C [A] MOL2 format, chain B [A] MOL2 format, chain C [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A]	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction