International Institute ofMolecular and Cell BiologyWarsaw, Poland

Max-Planck Institute ofMolecular Cell Biology and Genetics

Dresden, Germany

Laboratory of Structural BiologyMax-Planck-PAN Joint Junior Research Group

Physics in Biology:

Protein Crystallography

From physics to biology

Crystallography of sapphire

Walther group, Munich

Protein crystallography

Warsaw

10 108 10-8

Crystallography shows tremendous complexity at high magnification.

Bacterial cell walls

Gram negative Gram positive

membranemembrane

peptidoglycanpeptidoglycan

membrane

Peptidoglycan detail

N-domain catalytic domain C-domainlysostaphin

LytM

HxH

HxH

LytM was studied as a model system for lysostaphin.

LytM is a new fold in proteolysis

N-domain

C-domain

Zinc ligands:

H 210D 214H 293

Occluding ligand:

N117

S. G. Odintsov, I. Sabala, M. Marcyjaniak, and M. Bochtler, Latent LytM at 1.3A resolution. J Mol Biol, 2004. 335(3): p. 775-85.

LytM, mature form

D-Ala-D-Ala carboxypeptidase

Sonic hedgehog, N-domain

Bochtler M, Odintsov SG, Marcyjaniak M, Sabala I. Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases. Protein Sci. 2004 13 (4): p. 854-61.

Unexpected local similarities

HX3-6D

HXH

MepA-type enzymes could be LAS enzymes.

LytM (active form) MepA

D-Ala-D-Ala

carboxypeptidase

VanX

Sonic hedgehog

N-domain

Summary: the LAS group so far

Another unknown peptidoglycan amidase, unknown fold and function

blue highest conservation, red lowest conservation

Korza HJ, Bochtler M. P. aeruginosa LD-carboxypeptidase: A serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J Biol Chem. 2005 Sep 14; [Epub ahead of print]

A serine peptidase with a Ser-His-Glu triad.

Note that mutated enzymes were used in 100-fold higher concentration and incubated longer than wild-type enzyme to make the comparison more stringent.

The active site serines are Ramachandran outliers.

LD-carboxypeptidase

-hydrolase

(in this case, a lipase)

Acknowledgement: