7P6S

Crystal structure of the FimH-binding decoy module of human glycoprotein 2 (GP2) (crystal form II)

PDB DOI: https://doi.org/10.2210/pdb7P6S/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-07-17 Released: 2022-03-16
Deposition Author(s): Stsiapanava, A., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Jovine, L.
Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.224
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.

Stsiapanava, A., Xu, C., Nishio, S., Han, L., Yamakawa, N., Carroni, M., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Wu, B., Jovine, L.

(2022) Nat Struct Mol Biol 29: 190-193

PubMed: 35273390 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-022-00729-3
Primary Citation of Related Structures:
7P6R, 7P6S, 7P6T, 7PFP, 7Q3N

PubMed Abstract:

Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy.

Related Citations:

Glycoprotein synthesis in the adult rat pancreas. IV. Subcellular distribution of membrane glycoproteins.
Ronzio, R.A., Kronquist, K.E., Lewis, D.S., MacDonald, R.J., Mohrlok, S.H., O'Donnell Jr., J.J.
(1978) Biochim Biophys Acta 508: 65

Molecular cloning and sequences of cDNAs encoding alpha (large) and beta (small) isoforms of human pancreatic zymogen granule membrane-associated protein GP2.
Fukuoka, S.
(2000) Biochim Biophys Acta 1491: 376

GP2/THP gene family of self-binding, GPI-anchored proteins forms a cluster at chromosome 7F1 region in mouse genome.
Kobayashi, K., Yanagihara, K., Ishiguro, K., Fukuoka, S.
(2004) Biochem Biophys Res Commun 322: 659

Identification and characterization of D8C, a novel domain present in liver-specific LZP, uromodulin and glycoprotein 2, mutated in familial juvenile hyperuricaemic nephropathy.
Yang, H., Wu, C., Zhao, S., Guo, J.
(2004) FEBS Lett 578: 236

The pancreatic zymogen granule membrane protein, GP2, binds Escherichia coli Type 1 fimbriae.
Yu, S., Lowe, A.W.
(2009) BMC Gastroenterol 9: 58

Uptake through glycoprotein 2 of FimH(+) bacteria by M cells initiates mucosal immune response.
Hase, K., Kawano, K., Nochi, T., Pontes, G.S., Fukuda, S., Ebisawa, M., Kadokura, K., Tobe, T., Fujimura, Y., Kawano, S., Yabashi, A., Waguri, S., Nakato, G., Kimura, S., Murakami, T., Iimura, M., Hamura, K., Fukuoka, S., Lowe, A.W., Itoh, K., Kiyono, H., Ohno, H.
(2009) Nature 462: 226

Identification of GP2, the major zymogen granule membrane glycoprotein, as the autoantigen of pancreatic antibodies in Crohn's disease.
Roggenbuck, D., Hausdorf, G., Martinez-Gamboa, L., Reinhold, D., Buttner, T., Jungblut, P.R., Porstmann, T., Laass, M.W., Henker, J., Buning, C., Feist, E., Conrad, K.
(2009) Gut 58: 1620

Autoantibodies to GP2, the major zymogen granule membrane glycoprotein, in patients with gluten-sensitive enteropathy: a possible serological trap.
Bonaci-Nikolic, B., Spuran, M., Andrejevic, S., Nikolic, M.
(2012) Clin Chim Acta 413: 822

Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Zidek, A., Potapenko, A., Bridgland, A., Senior, A.W., Meyer, C., Kavukcuoglu, K., Kohl, S.A.A., Kohli, P., Ballard, A.J., Hassabis, D., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O.
(2021) Nature --: --

Organizational Affiliation:

School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. luca.jovine@ki.se.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Alpha of Pancreatic secretory granule membrane major glycoprotein GP2	A	161	Homo sapiens	Mutation(s): 0 Gene Names: GP2
UniProt & NIH Common Fund Data Resources
Find proteins for P55259 (Homo sapiens) Explore P55259 Go to UniProtKB: P55259
PHAROS: P55259
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55259
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A]	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
9JE Query on 9JE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	pentane-1,5-diol C₅ H₁₂ O₂ ALQSHHUCVQOPAS-UHFFFAOYSA-N		Ligand Interaction