Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development

EMBO J. 1995 Dec 1;14(23):5947-56.


Xenopus nuclear factor XNF7, a maternally expressed protein, functions in patterning of the embryo. XNF7 contains a number of defined protein domains implicated in the regulation of some developmental processes. Among these is a tripartite motif comprising a zinc-binding RING finger and B-box domain next to a predicted alpha-helical coiled-coil domain. Interestingly, this motif is found in a variety of protein including several proto-oncoproteins. Here we describe the solution structure of the XNF7 B-box zinc-binding domain determined at physiological pH by 1H NMR methods. The B-box structure represents the first three-dimensional structure of this new motif and comprises a monomer have two beta-strands, two helical turns and three extended loop regions packed in a novel topology. The r.m.s. deviation for the best 18 structures is 1.15 A for backbone atoms and 1.94 A for all atoms. Structure calculations and biochemical data shows one zinc atom ligated in a Cys2-His2 tetrahedral arrangement. We have used mutant peptides to determine the metal ligation scheme which surprisingly shows that not all of the seven conserved cysteines/histidines in the B-box motif are involved in metal ligation. The B-box structure is not similar in tertiary fold to any other known zinc-binding motif.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Computer Graphics
  • DNA-Binding Proteins
  • Egg Proteins
  • Hydrogen Bonding
  • Iron / metabolism
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Proteins / chemistry*
  • Peptides / chemistry
  • Phosphoproteins / chemistry*
  • Protein Conformation
  • Protein Structure, Secondary
  • Sequence Alignment
  • Xenopus / embryology
  • Xenopus Proteins*
  • Zinc / metabolism*
  • Zinc Fingers*


  • DNA-Binding Proteins
  • Egg Proteins
  • Nuclear Proteins
  • Peptides
  • Phosphoproteins
  • Xenopus Proteins
  • XNF7 protein, Xenopus
  • Iron
  • Zinc