6LNA

YdiU complex with AMPNPP and Mn2+

Summary for 6LNA

• Entry DOI: 10.2210/pdb6lna/pdb
• Descriptor: Protein adenylyltransferase SelO, MANGANESE (II) ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (5 entities in total)
• Functional Keywords: complex, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 110272.31

Authors

Li, B.,Yang, Y.,Ma, Y. (deposition date: 2019-12-28, release date: 2020-12-30, Last modification date: 2023-11-22)

Primary citation

Yang, Y.,Yue, Y.,Song, N.,Li, C.,Yuan, Z.,Wang, Y.,Ma, Y.,Li, H.,Zhang, F.,Wang, W.,Jia, H.,Li, P.,Li, X.,Wang, Q.,Ding, Z.,Dong, H.,Gu, L.,Li, B.
The YdiU Domain Modulates Bacterial Stress Signaling through Mn 2+ -Dependent UMPylation.
Cell Rep, 32:108161-108161, 2020

PubMed Abstract: Sensing stressful conditions and adjusting the cellular metabolism to adapt to the environment are essential activities for bacteria to survive in variable situations. Here, we describe a stress-related protein, YdiU, and characterize YdiU as an enzyme that catalyzes the covalent attachment of uridine-5'-monophosphate to a protein tyrosine/histidine residue, an unusual modification defined as UMPylation. Mn serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn binding converts YdiU to an aggregate-prone state facilitating the recruitment of chaperones. The UMPylation of chaperones prevents them from binding co-factors or clients, thereby impairing their function. Consistent with the recent finding that YdiU acts as an AMPylator, we further demonstrate that the self-AMPylation of YdiU padlocks its chaperone-UMPylation activity. A detailed mechanism is proposed based on the crystal structures of Apo-YdiU and YdiU-AMPNPP-Mn and on molecular dynamics simulation models of YdiU-UTP-Mn and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation.

PubMed: 32966796
DOI: 10.1016/j.celrep.2020.108161

Experimental method

X-RAY DIFFRACTION (1.701 Å)