7D72

Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-Mannose


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.

Zheng, L.Liu, Z.Wang, Y.Yang, F.Wang, J.Huang, W.Qin, J.Tian, M.Cai, X.Liu, X.Mo, X.Gao, N.Jia, D.

(2021) Nat Struct Mol Biol 28: 1-12

  • DOI: https://doi.org/10.1038/s41594-021-00591-9
  • Primary Citation of Related Structures:  
    7D72, 7D73, 7D74

  • PubMed Abstract: 

    GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation and glycophosphatidylinositol anchor synthesis, and aberrant cellular GDP-Man levels have been associated with multiple human diseases. How cells maintain homeostasis of GDP-Man is unknown. Here, we report the cryo-EM structures of human GMPPA-GMPPB complex, the protein machinery responsible for GDP-Man synthesis, in complex with GDP-Man or GTP. Unexpectedly, we find that the catalytically inactive subunit GMPPA displays a much higher affinity to GDP-Man than the active subunit GMPPB and, subsequently, inhibits the catalytic activity of GMPPB through a unique C-terminal loop of GMPPA. Importantly, disruption of the interactions between GMPPA and GMPPB or the binding of GDP-Man to GMPPA in zebrafish leads to abnormal brain development and muscle abnormality, analogous to phenotypes observed in individuals carrying GMPPA or GMPPB mutations. We conclude that GMPPA acts as a cellular sensor to maintain mannose homeostasis through allosterically regulating GMPPB.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannose-1-phosphate guanyltransferase beta360Homo sapiensMutation(s): 0 
Gene Names: GMPPB
EC: 2.7.7.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5P6 (Homo sapiens)
Explore Q9Y5P6 
Go to UniProtKB:  Q9Y5P6
PHAROS:  Q9Y5P6
GTEx:  ENSG00000173540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5P6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mannose-1-phosphate guanyltransferase alphaC [auth A],
D [auth B],
E [auth C],
F [auth D]
420Homo sapiensMutation(s): 0 
Gene Names: GMPPA
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IJ6 (Homo sapiens)
Explore Q96IJ6 
Go to UniProtKB:  Q96IJ6
PHAROS:  Q96IJ6
GTEx:  ENSG00000144591 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96IJ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDD (Subject of Investigation/LOI)
Query on GDD

Download Ideal Coordinates CCD File 
AA [auth L]
M [auth K]
N [auth I]
O [auth A]
P [auth B]
AA [auth L],
M [auth K],
N [auth I],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
U [auth F],
W [auth G],
Y [auth H],
Z [auth J]
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
T [auth E],
V [auth F],
X [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary