PDBsum entry 1df8

Binding protein

PDB id

1df8

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Contents

			Protein chains

					118 a.a. *

			Ligands

					BTN ×2

			Waters ×320

* Residue conservation analysis

PDB id:

1df8

Links

Name:

Binding protein

Title:

S45a mutant of streptavidin in complex with biotin

Structure:

Protein (streptavidin). Chain: a, b. Fragment: core, residues 13-139. Synonym: core streptavidin. Engineered: yes. Mutation: yes

Source:

Streptomyces avidinii. Organism_taxid: 1895. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.51Å

R-factor:

0.169

R-free:

0.225

Authors:

D.E.Hyre,I.Le Trong,S.Freitag,R.E.Stenkamp,P.S.Stayton

Key ref:

D.E.Hyre et al. (2000). Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system. Protein Sci, 9, 878-885. PubMed id: 10850797 DOI: 10.1110/ps.9.5.878

Date:

18-Nov-99

Release date:

20-Sep-00

PROCHECK

	Headers

	References

Protein chains

P22629 (SAV_STRAV) - Streptavidin from Streptomyces avidinii

Seq: Struc:					183 a.a. 118 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1110/ps.9.5.878	Protein Sci 9:878-885 (2000)
PubMed id: 10850797

Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system.
D.E.Hyre, I.Le Trong, S.Freitag, R.E.Stenkamp, P.S.Stayton.

ABSTRACT

The contribution of the Ser45 hydrogen bond to biotin binding activation and equilibrium thermodynamics was investigated by biophysical and X-ray crystallographic studies. The S45A mutant exhibits a 1,700-fold greater dissociation rate and 907-fold lower equilibrium affinity for biotin relative to wild-type streptavidin at 37 degrees C, indicating a crucial role in binding energetics. The crystal structure of the biotin-bound mutant reveals only small changes from the wild-type bound structure, and the remaining hydrogen bonds to biotin retain approximately the same lengths. No additional water molecules are observed to replace the missing hydroxyl, in contrast to the previously studied D128A mutant. The equilibrium deltaG degrees, deltaH degrees, deltaS degrees, deltaC degrees(p), and activation deltaG++ of S45A at 37 degrees C are 13.7+/-0.1 kcal/mol, -21.1+/-0.5 kcal/mol, -23.7+/-1.8 cal/mol K, -223+/-12 cal/mol K, and 20.0+/-2.5 kcal/mol, respectively. Eyring analysis of the large temperature dependence of the S45A off-rate resolves the deltaH++ and deltaS++ of dissociation, 25.8+/-1.2 kcal/mol and 18.7+/-4.3 cal/mol K. The large increases of deltaH++ and deltaS++ in the mutant, relative to wild-type, indicate that Ser45 could form a hydrogen bond with biotin in the wild-type dissociation transition state, enthalpically stabilizing it, and constraining the transition state entropically. The postulated existence of a Ser45-mediated hydrogen bond in the wild-type streptavidin transition state is consistent with potential of mean force simulations of the dissociation pathway and with molecular dynamics simulations of biotin pullout, where Ser45 is seen to form a hydrogen bond with the ureido oxygen as biotin slips past this residue after breaking the native hydrogen bonds.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21305032

J.Leppiniemi, J.A.Määttä, H.Hammaren, M.Soikkeli, M.Laitaoja, J.Jänis, M.S.Kulomaa, and V.P.Hytönen (2011).
Bifunctional avidin with covalently modifiable ligand binding site.

PLoS One, 6, e16576.

20383133

C.E.Chivers, E.Crozat, C.Chu, V.T.Moy, D.J.Sherratt, and M.Howarth (2010).
A streptavidin variant with slower biotin dissociation and increased mechanostability.

Nat Methods, 7, 391-393.

21041662

H.Hong, T.M.Blois, Z.Cao, and J.U.Bowie (2010).
Method to measure strong protein-protein interactions in lipid bilayers using a steric trap.

Proc Natl Acad Sci U S A, 107, 19802-19807.

20526651

J.J.Panek, T.R.Ward, A.Jezierska-Mazzarello, and M.Novic (2010).
Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin-an insight from molecular dynamics simulations with classical and ab initio force fields.

J Comput Aided Mol Des, 24, 719-732.

19425594

A.A.Edwards, J.M.Mason, K.Clinch, P.C.Tyler, G.B.Evans, and V.L.Schramm (2009).
Altered enthalpy-entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase.

Biochemistry, 48, 5226-5238.

19374419

D.S.Cerutti, I.Le Trong, R.E.Stenkamp, and T.P.Lybrand (2009).
Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.

J Phys Chem B, 113, 6971-6985.

19739627

T.M.Blois, H.Hong, T.H.Kim, and J.U.Bowie (2009).
Protein unfolding with a steric trap.

J Am Chem Soc, 131, 13914-13915.

18178658

E.B.Walton, S.Lee, and K.J.Van Vliet (2008).
Extending Bell's model: how force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes.

Biophys J, 94, 2621-2630.

17417839

J.DeChancie, and K.N.Houk (2007).
The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site.

J Am Chem Soc, 129, 5419-5429.

16452627

D.E.Hyre, I.Le Trong, E.A.Merritt, J.F.Eccleston, N.M.Green, R.E.Stenkamp, and P.S.Stayton (2006).
Cooperative hydrogen bond interactions in the streptavidin-biotin system.

Protein Sci, 15, 459-467.

PDB codes:

1mep 1mk5

16699183

I.Le Trong, D.G.Aubert, N.R.Thomas, and R.E.Stenkamp (2006).
The high-resolution structure of (+)-epi-biotin bound to streptavidin.

Acta Crystallogr D Biol Crystallogr, 62, 576-581.

PDB codes:

2f01 2gh7

16554831

M.Howarth, D.J.Chinnapen, K.Gerrow, P.C.Dorrestein, M.R.Grandy, N.L.Kelleher, A.El-Husseini, and A.Y.Ting (2006).
A monovalent streptavidin with a single femtomolar biotin binding site.

Nat Methods, 3, 267-273.

16175628

V.P.Hytönen, H.R.Nordlund, J.Hörhä, T.K.Nyholm, D.E.Hyre, T.Kulomaa, E.J.Porkka, A.T.Marttila, P.S.Stayton, O.H.Laitinen, and M.S.Kulomaa (2005).
Dual-affinity avidin molecules.

Proteins, 61, 597-607.

16212654

V.P.Hytönen, J.A.Määttä, H.Kidron, K.K.Halling, J.Hörhä, T.Kulomaa, T.K.Nyholm, M.S.Johnson, T.A.Salminen, M.S.Kulomaa, and T.T.Airenne (2005).
Avidin related protein 2 shows unique structural and functional features among the avidin protein family.

BMC Biotechnol, 5, 28.

PDB code:

1wbi

15593167

D.H.Williams, E.Stephens, D.P.O'Brien, and M.Zhou (2004).
Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes.

Angew Chem Int Ed Engl, 43, 6596-6616.

12925786

I.Le Trong, S.Freitag, L.A.Klumb, V.Chu, P.S.Stayton, and R.E.Stenkamp (2003).
Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.

Acta Crystallogr D Biol Crystallogr, 59, 1567-1573.

PDB codes:

1n43 1n4j 1n7y 1n9m 1n9y 1nbx 1nc9 1ndj

12134141

D.E.Hyre, L.M.Amon, J.E.Penzotti, I.Le Trong, R.E.Stenkamp, T.P.Lybrand, and P.S.Stayton (2002).
Early mechanistic events in biotin dissociation from streptavidin.

Nat Struct Biol, 9, 582-585.

11847279

K.Kwon, E.D.Streaker, and D.Beckett (2002).
Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase.

Protein Sci, 11, 558-570.

11259306

M.C.Williams, J.R.Wenner, I.Rouzina, and V.A.Bloomfield (2001).
Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching.

Biophys J, 80, 1932-1939.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.