6T1B | pdb_00006t1b

Crystal structure of YlmD from Geobacillus stearothermophilus in complex with inosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle.

Cader, M.Z.de Almeida Rodrigues, R.P.West, J.A.Sewell, G.W.Md-Ibrahim, M.N.Reikine, S.Sirago, G.Unger, L.W.Iglesias-Romero, A.B.Ramshorn, K.Haag, L.M.Saveljeva, S.Ebel, J.F.Rosenstiel, P.Kaneider, N.C.Lee, J.C.Lawley, T.D.Bradley, A.Dougan, G.Modis, Y.Griffin, J.L.Kaser, A.

(2020) Cell 180: 278

  • DOI: https://doi.org/10.1016/j.cell.2019.12.017
  • Primary Citation Related Structures: 
    6T0Y, 6T1B

  • PubMed Abstract: 

    Mutations in FAMIN cause arthritis and inflammatory bowel disease in early childhood, and a common genetic variant increases the risk for Crohn's disease and leprosy. We developed an unbiased liquid chromatography-mass spectrometry screen for enzymatic activity of this orphan protein. We report that FAMIN phosphorolytically cleaves adenosine into adenine and ribose-1-phosphate. Such activity was considered absent from eukaryotic metabolism. FAMIN and its prokaryotic orthologs additionally have adenosine deaminase, purine nucleoside phosphorylase, and S-methyl-5'-thioadenosine phosphorylase activity, hence, combine activities of the namesake enzymes of central purine metabolism. FAMIN enables in macrophages a purine nucleotide cycle (PNC) between adenosine and inosine monophosphate and adenylosuccinate, which consumes aspartate and releases fumarate in a manner involving fatty acid oxidation and ATP-citrate lyase activity. This macrophage PNC synchronizes mitochondrial activity with glycolysis by balancing electron transfer to mitochondria, thereby supporting glycolytic activity and promoting oxidative phosphorylation and mitochondrial H + and phosphate recycling.


  • Organizational Affiliation
    • Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.

Macromolecule Content 

  • Total Structure Weight: 30.33 kDa 
  • Atom Count: 2,317 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 275 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YlmD275Geobacillus stearothermophilusMutation(s): 0 
EC: 2.4.2.1 (UniProt), 3.5.4.4 (UniProt), 2.4.2.28 (UniProt)
UniProt
Find proteins for P84138 (Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10))
Explore P84138 
Go to UniProtKB:  P84138
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84138
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.556α = 90
b = 48.483β = 90
c = 134.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101908/Z/13/Z
Wellcome TrustUnited Kingdom217191/Z/19/Z
Wellcome TrustUnited Kingdom106260/Z/14/Z
European Research Council (ERC)United KingdomHORIZON2020/ERC 648889
European Research Council (ERC)United KingdomFP7/2007-2013 260961

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description