PDBsum entry 3k2u

Hydrolase/immune system

PDB id: 3k2u

Contents

Protein chains

233 a.a. *

215 a.a. *

208 a.a. *

Ligands

ALA-CYS-GLY-ARG-ARG

NAG-NAG

Waters ×168

* Residue conservation analysis

PDB id:

3k2u

Name:

Hydrolase/immune system

Title:

Crystal structure of hgfa in complex with the allosteric inhibitory antibody fab40

Structure:

Hepatocyte growth factor activator long chain. Chain: a. Synonym: hgf activator, hgfa. Engineered: yes. Hepatocyte growth factor activator short chain. Chain: b. Synonym: hgf activator, hgfa. Engineered: yes. Antibody, fab fragment, heavy chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.239 R-free: 0.290

Authors:

R.Ganesan,C.Eigenbrot,S.Shia

Key ref:

R.Ganesan et al. (2009). Unraveling the allosteric mechanism of serine protease inhibition by an antibody. Structure, 17, 1614-1624. PubMed id: 20004165

Date:

30-Sep-09 Release date: 15-Dec-09

Protein chain

Q04756  (HGFA_HUMAN) -  Hepatocyte growth factor activator from Homo sapiens

Seq: 655 a.a.

Struc: 233 a.a.

Protein chain

No UniProt id for this chain

Struc: 215 a.a.

Protein chain

No UniProt id for this chain

Struc: 208 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.- - ?????

Structure 17:1614-1624 (2009)

PubMed id: 20004165

Unraveling the allosteric mechanism of serine protease inhibition by an antibody.

R.Ganesan, C.Eigenbrot, Y.Wu, W.C.Liang, S.Shia, M.T.Lipari, D.Kirchhofer.

ABSTRACT

Recent structural studies have outlined the mechanism of protease inhibition by active site-directed antibodies. However, the molecular basis of allosteric inhibition by antibodies has been elusive. Here we report the 2.35 A resolution structure of the trypsin-like serine protease hepatocyte growth factor activator (HGFA) in complex with the allosteric antibody Ab40, a potent inhibitor of HGFA catalytic activity. The antibody binds at the periphery of the substrate binding cleft and imposes a conformational change on the entire 99-loop (chymotrypsinogen numbering). The altered conformation of the 99-loop is incompatible with substrate binding due to the partial collapse of subsite S2 and the reorganization of subsite S4. Remarkably, a single residue deletion of Ab40 abolished inhibition of HGFA activity, commensurate with the reversal of the 99-loop conformation to its "competent" state. The results define an "allosteric switch" mechanism as the basis of protease inhibition by an allosteric antibody.