2H5D

0.9A resolution crystal structure of alpha-lytic protease complexed with a transition state analogue, MeOSuc-Ala-Ala-Pro-Val boronic acid

Summary for 2H5D

• Entry DOI: 10.2210/pdb2h5d/pdb
• Related: 1P03 1QRX 1SSX 1TAL 2H5C 2ULL
• Related PRD ID: PRD_000316
• Descriptor: ALPHA-LYTIC PROTEASE, MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID INHIBITOR, SULFATE ION, ... (5 entities in total)
• Functional Keywords: a-lytic protease, serine protease, acylation transition state, catalysis, protein folding, protein stability, packing distortion, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Lysobacter enzymogenes
• Total number of polymer chains: 2
• Total formula weight: 21206.05

Authors

Fuhrmann, C.N.,Agard, D.A. (deposition date: 2006-05-25, release date: 2006-09-26, Last modification date: 2024-11-20)

Primary citation

Fuhrmann, C.N.,Daugherty, M.D.,Agard, D.A.
Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis
J.Am.Chem.Soc., 128:9086-9102, 2006

PubMed Abstract: To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of alpha-lytic protease (alphaLP) that mimic aspects of the transition states: alphaLP at pH 5 (0.82 A resolution) and alphaLP bound to the peptidyl boronic acid inhibitor, MeOSuc-Ala-Ala-Pro-boroVal (0.90 A resolution). Based on these structures, there is no evidence of, or requirement for, histidine-flipping during the acylation step of the reaction. Rather, our data suggests that upon protonation of His57, Ser195 undergoes a conformational change that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102 hydrogen bond in the catalytic triad is a normal ionic hydrogen bond, and not a low-barrier hydrogen bond (LBHB) as previously hypothesized. We propose that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states. In particular, a short ionic hydrogen bond (SIHB) between His57 Nepsilon2 and the substrate's leaving group may promote forward progression of the TI1-to-acylenzyme reaction. We provide experimental evidence that refutes use of either a short donor-acceptor distance or a downfield 1H chemical shift as sole indicators of a LBHB.

PubMed: 16834383
DOI: 10.1021/ja057721o

Experimental method

X-RAY DIFFRACTION (0.9 Å)