6LNA

YdiU complex with AMPNPP and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.143 

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Literature

The YdiU Domain Modulates Bacterial Stress Signaling through Mn 2+ -Dependent UMPylation.

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.

(2020) Cell Rep 32: 108161-108161

  • DOI: 10.1016/j.celrep.2020.108161
  • Primary Citation of Related Structures:  
    6LNA

  • 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 ...

    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 2+ serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn 2+ 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 2+ and on molecular dynamics simulation models of YdiU-UTP-Mn 2+ and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation.


    Organizational Affiliation

    Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China. Electronic address: bingqingsdu@163.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein adenylyltransferase SelOA, B478Escherichia coliMutation(s): 1 
Gene Names: 
EC: 2.7.7
UniProt
Find proteins for P77649 (Escherichia coli (strain K12))
Explore P77649 
Go to UniProtKB:  P77649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77649
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.143 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.43α = 90
b = 73.541β = 102.49
c = 122.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2019-12-28 
  • Released Date: 2020-12-30 
  • Deposition Author(s): Li, B., Yang, Y., Ma, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references