PDBsum entry 1xf7

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protein metals links
Transcription PDB id
Protein chain
29 a.a.
PDB id:
Name: Transcription
Title: High resolution nmr structure of the wilms' tumor suppressor protein (wt1) finger 3
Structure: Wilms' tumor protein. Chain: a. Fragment: zinc finger 3. Synonym: wt33. Wilms' tumor suppressor protein. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: synthesized by solid-phase synthesis. The sequence occurs naturally homo sapiens (human). The g28e and t29k mutations improve sample behavior without affecting the structure
NMR struc: 40 models
Authors: M.J.Lachenmann,J.E.Ladbury,J.Dong,K.Huang,P.Carey,M.A.Weiss
Key ref:
M.J.Lachenmann et al. (2004). Why zinc fingers prefer zinc: ligand-field symmetry and the hidden thermodynamics of metal ion selectivity. Biochemistry, 43, 13910-13925. PubMed id: 15518539 DOI: 10.1021/bi0491999
14-Sep-04     Release date:   14-Dec-04    
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Protein chain
Pfam   ArchSchema ?
P19544  (WT1_HUMAN) -  Wilms tumor protein
449 a.a.
29 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)


DOI no: 10.1021/bi0491999 Biochemistry 43:13910-13925 (2004)
PubMed id: 15518539  
Why zinc fingers prefer zinc: ligand-field symmetry and the hidden thermodynamics of metal ion selectivity.
M.J.Lachenmann, J.E.Ladbury, J.Dong, K.Huang, P.Carey, M.A.Weiss.
The zinc finger, a motif of protein-nucleic acid recognition broadly conserved among eukaryotes, is a globular minidomain containing a tetrahedral metal-binding site. Preferential coordination of Zn(2+) (relative to Co(2+)) is proposed to reflect differences in ligand-field stabilization energies (LFSEs) due to complete or incomplete occupancy of d orbitals. LFSE predicts that the preference for Zn(2+) should be purely enthalpic in accord with calorimetric studies of a high-affinity consensus peptide (CP-1; Blasie, C. A., and Berg, J. (2002) Biochemistry 41, 15068-73). Despite its elegance, the general predominance of LFSE is unclear as (i) the magnitude by which CP-1 prefers Zn(2+) is greater than that expected and (ii) the analogous metal ion selectivity of a zinc metalloenzyme (carbonic anhydrase) is driven by changes in entropy rather than enthalpy. Because CP-1 was designed to optimize zinc binding, we have investigated the NMR structure and metal ion selectivity of a natural finger of lower stability derived from human tumor-suppressor protein WT1. Raman spectroscopy suggests that the structure of the WT1 domain is unaffected by interchange of Zn(2+) and Co(2+). As in CP-1, preferential binding of Zn(2+) (relative to Co(2+)) is driven predominantly by differences in enthalpy, but in this case the enthalpic advantage is less than that predicted by LFSE. A theoretical framework is presented to define the relationship between LFSE and other thermodynamic factors, such as metal ion electroaffinities, enthalpies of hydration, and the topography of the underlying folding landscape. The contribution of environmental coupling to entropy-enthalpy compensation is delineated in a formal thermodynamic cycle. Together, these considerations indicate that LFSE provides an important but incomplete description of the stringency and thermodynamic origin of metal-ion selectivity.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21253649 S.M.Quintal, Q.A.dePaula, and N.P.Farrell (2011).
Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences.
  Metallomics, 3, 121-139.  
20050606 G.D.Straganz, A.R.Diebold, S.Egger, B.Nidetzky, and E.I.Solomon (2010).
Kinetic and CD/MCD spectroscopic studies of the atypical, three-His-ligated, non-heme Fe2+ center in diketone dioxygenase: the role of hydrophilic outer shell residues in catalysis.
  Biochemistry, 49, 996.  
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
19859605 E.Almaraz, J.A.Denny, W.S.Foley, J.H.Reibenspies, N.Bhuvanesh, and M.Y.Darensbourg (2009).
Zinc/nickel exchange and ligand cannibalism in N2S2O(1,2) donor ligand sets.
  Dalton Trans, (), 9496-9502.  
18648687 A.I.Anzellotti, and N.P.Farrell (2008).
Zinc metalloproteins as medicinal targets.
  Chem Soc Rev, 37, 1629-1651.  
18461372 K.D.Weaver, J.J.Heymann, A.Mehta, P.L.Roulhac, D.S.Anderson, A.J.Nowalk, P.Adhikari, T.A.Mietzner, M.C.Fitzgerald, and A.L.Crumbliss (2008).
Ga3+ as a mechanistic probe in Fe3+ transport: characterization of Ga3+ interaction with FbpA.
  J Biol Inorg Chem, 13, 887-898.  
18287285 P.L.Hayes, B.L.Lytle, B.F.Volkman, and F.C.Peterson (2008).
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein.
  Protein Sci, 17, 571-576.
PDB code: 1zr9
17928348 J.York, and J.H.Nunberg (2007).
A novel zinc-binding domain is essential for formation of the functional Junín virus envelope glycoprotein complex.
  J Virol, 81, 13385-13391.  
17977509 K.T.Nguyen, J.C.Wu, J.A.Boylan, F.C.Gherardini, and D.Pei (2007).
Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase.
  Arch Biochem Biophys, 468, 217-225.  
16291661 Y.Lin, J.B.Robbins, E.K.Nyannor, Y.H.Chen, and I.K.Cann (2005).
A CCCH zinc finger conserved in a replication protein a homolog found in diverse Euryarchaeotes.
  J Bacteriol, 187, 7881-7889.  
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