3N75

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI

Summary for 3N75

• Entry DOI: 10.2210/pdb3n75/pdb
• Descriptor: Lysine decarboxylase, inducible, GUANOSINE-5',3'-TETRAPHOSPHATE, HEXAETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: pyridoxal-5'-phosphate dependent decarboxylase, acid stress response, stringent response, guanosine tetraphosphate (ppgpp), lyase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm (Probable): P0A9H3
• Total number of polymer chains: 5
• Total formula weight: 412813.55

Authors

Kanjee, U.,Alexopoulos, E.,Pai, E.F.,Houry, W.A. (deposition date: 2010-05-26, release date: 2011-02-16, Last modification date: 2023-11-22)

Primary citation

Kanjee, U.,Gutsche, I.,Alexopoulos, E.,Zhao, B.,El Bakkouri, M.,Thibault, G.,Liu, K.,Ramachandran, S.,Snider, J.,Pai, E.F.,Houry, W.A.
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.
Embo J., 30:931-944, 2011

PubMed Abstract: The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH∼5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.

PubMed: 21278708
DOI: 10.1038/emboj.2011.5

Experimental method

X-RAY DIFFRACTION (2 Å)