6HPV

Crystal structure of mouse fetuin-B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition.

Cuppari, A.Korschgen, H.Fahrenkamp, D.Schmitz, C.Guevara, T.Karmilin, K.Kuske, M.Olf, M.Dietzel, E.Yiallouros, I.de Sanctis, D.Goulas, T.Weiskirchen, R.Jahnen-Dechent, W.Floehr, J.Stoecker, W.Jovine, L.Gomis-Ruth, F.X.

(2019) IUCrJ 6: 317-330

  • DOI: 10.1107/S2052252519001568
  • Primary Citation of Related Structures:  
    6HPV, 6HT9

  • PubMed Abstract: 
  • Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility ...

    Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWV X GP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWV X GP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.


    Related Citations: 
    • Fetuin-B, a second member of the fetuin family in mammals.
      Olivier, E., Soury, E., Ruminy, P., Husson, A., Parmentier, F., Daveau, M., Salier, J.P.
      (2000) Biochem J 350 Pt 2: 589
    • Tissue distribution and activity testing suggest a similar but not identical function of fetuin-B and fetuin-A.
      Denecke, B., Graber, S., Schafer, C., Heiss, A., Woltje, M., Jahnen-Dechent, W.
      (2003) Biochem J 376: 135
    • Fetuin-B, a liver-derived plasma protein is essential for fertilization.
      Dietzel, E., Wessling, J., Floehr, J., Schafer, C., Ensslen, S., Denecke, B., Rosing, B., Neulen, J., Veitinger, T., Spehr, M., Tropartz, T., Tolba, R., Renne, T., Egert, A., Schorle, H., Gottenbusch, Y., Hildebrand, A., Yiallouros, I., Stocker, W., Weiskirchen, R., Jahnen-Dechent, W.
      (2013) Dev Cell 25: 106
    • Mammalian gamete fusion depends on the inhibition of ovastacin by fetuin-B.
      Stocker, W., Karmilin, K., Hildebrand, A., Westphal, H., Yiallouros, I., Weiskirchen, R., Dietzel, E., Floehr, J., Jahnen-Dechent, W.
      (2014) Biol Chem 395: 1195
    • Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.
      Meex, R.C., Hoy, A.J., Morris, A., Brown, R.D., Lo, J.C., Burke, M., Goode, R.J., Kingwell, B.A., Kraakman, M.J., Febbraio, M.A., Greve, J.W., Rensen, S.S., Molloy, M.P., Lancaster, G.I., Bruce, C.R., Watt, M.J.
      (2015) Cell Metab 22: 1078
    • Association of high fetuin-B concentrations in serum with fertilization rate in IVF: a cross-sectional pilot study.
      Floehr, J., Dietzel, E., Neulen, J., Rosing, B., Weissenborn, U., Jahnen-Dechent, W.
      (2016) Hum Reprod 31: 630
    • Recombinant fetuin-B protein maintains high fertilization rate in cumulus cell-free mouse oocytes.
      Dietzel, E., Floehr, J., Van de Leur, E., Weiskirchen, R., Jahnen-Dechent, W.
      (2017) Mol Hum Reprod 23: 25
    • The novel adipokine/hepatokine fetuin B in severe human and murine diabetic kidney disease.
      Kralisch, S., Hoffmann, A., Kloting, N., Bachmann, A., Kratzsch, J., Bluher, M., Zhang, M.Z., Harris, R.C., Stumvoll, M., Fasshauer, M., Ebert, T.
      (2017) Diabetes Metab 43: 465
    • Maternal malnourishment induced upregulation of fetuin-B blunts nephrogenesis in the low birth weight neonate.
      Rabadi, M.M., Abdulmahdi, W., Nesi, L., Jules, E., Marghani, Y., Sheinin, E., Tilzer, J., Gupta, S., Chen, S., Cassimatis, N.D., Lipphardt, M., Kozlowski, P.B., Ratliff, B.B.
      (2018) Dev Biol 443: 78
    • Mammalian plasma fetuin-B is a selective inhibitor of ovastacin and meprin metalloproteinases.
      Karmilin, K., Schmitz, C., Kuske, M., Korschgen, H., Olf, M., Meyer, K., Hildebrand, A., Felten, M., Fridrich, S., Yiallouros, I., Becker-Pauly, C., Weiskirchen, R., Jahnen-Dechent, W., Floehr, J., Stocker, W.
      (2019) Sci Rep 9: 546

    Organizational Affiliation

    Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fetuin-BA378Mus musculusMutation(s): 0 
Gene Names: Fetub
Find proteins for Q9QXC1 (Mus musculus)
Explore Q9QXC1 
Go to UniProtKB:  Q9QXC1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.71α = 90
b = 67.71β = 90
c = 197.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03999
European Molecular Biology OrganizationGermany--
German Research Foundation--

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary