PDBsum entry 1slg

Complex(biotin-binding protein/peptide)

PDB id

1slg

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Contents

			Protein chains

					123 a.a. *

			Ligands

					SER-HIS-PRO-GLN- ASN-THR


					PHE-SER-HIS-PRO- GLN-ASN-THR

			Waters ×477

* Residue conservation analysis

PDB id:

1slg

Links

Name:

Complex(biotin-binding protein/peptide)

Title:

Streptavidin, ph 5.6, bound to peptide fchpqnt

Structure:

Streptavidin. Chain: b, d. Fchpqnt. Chain: m, p

Source:

Streptomyces avidinii. Organism_taxid: 1895.

Biol. unit:

60mer (from PQS)

Resolution:

1.76Å

R-factor:

0.187

R-free:

0.222

Authors:

B.A.Katz

Key ref:

B.A.Katz (1995). Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence. Biochemistry, 34, 15421-15429. PubMed id: 7492542

Date:

10-Mar-95

Release date:

03-Apr-96

PROCHECK

	Headers

	References

Protein chains

P22629 (SAV_STRAV) - Streptavidin from Streptomyces avidinii

Seq: Struc:					183 a.a. 123 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Biochemistry 34:15421-15429 (1995)
PubMed id: 7492542

Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence.
B.A.Katz.

ABSTRACT

The streptavidin-bound crystal structures of two disulfide-bridge cyclic peptides (cyclo-Ac-[CHPQGPPC]-NH2 and cyclo-Ac-[CHPQFC]-NH2) and of a linear peptide (FSHPQNT) were determined, as well as the structure of apostreptavidin (streptavidin-sulfate). Both the linear and disulfide-bridged cyclic peptides studied share a common HPQ conformation and make common interactions with streptavidin, although significant differences in structures and interactions occur for flanking residues among the complexes. The conformation of the linear peptide in the crystal structure of streptavidin-FSHPQNT was found to differ from that in the same complex published [Weber, P. C., Pantoliano, M. W., & Thompson, L. D. (1992) Biochemistry 31, 9350-9354]. In the present investigation, the HPQNT portion of the ligand is well-defined with some density defining the Phe, whereas in the investigation of Weber et al. only the HPQ segment of the bound peptide could be interpreted. Both bound cyclic peptides adopt a beta-turn involving an H-bond between the His main chain carbonyl and the main chain amide NH of the i+3 residue. In the streptavidin-bound cyclo-Ac-[CHPQFC]-NH2 structure, there is an additional H-bond, indicative of alpha-helix, between the main chain His carbonyl and the main chain C-terminal Cys amide NH group. Binding interactions for both cyclic and linear peptides include direct H-bonds, H-bonds mediated by tightly bound water molecules, and hydrophobic interactions. The above structures and that of streptavidin-biotin in the literature are compared and discussed in the context of structure-based ligand design.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21044268

D.Phichith, S.Bun, S.Padiolleau-Lefevre, A.Guellier, S.Banh, M.Galleni, J.M.Frere, D.Thomas, A.Friboulet, and B.Avalle (2010).
Novel peptide inhibiting both TEM-1 β-lactamase and penicillin-binding proteins.

FEBS J, 277, 4965-4972.

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.

19497129

M.Rajik, F.Jahanshiri, A.R.Omar, A.Ideris, S.S.Hassan, and K.Yusoff (2009).
Identification and characterisation of a novel anti-viral peptide against avian influenza virus H9N2.

Virol J, 6, 74.

19551843

Z.Cheng, and R.E.Campbell (2009).
An engineered tryptophan zipper-type peptide as a molecular recognition scaffold.

J Pept Sci, 15, 523-532.

18991423

Y.S.Sun, J.P.Landry, Y.Y.Fei, X.D.Zhu, J.T.Luo, X.B.Wang, and K.S.Lam (2008).
Effect of fluorescently labeling protein probes on kinetics of protein-ligand reactions.

Langmuir, 24, 13399-13405.

17763488

B.Helms, I.van Baal, M.Merkx, and E.W.Meijer (2007).
Site-specific protein and peptide immobilization on a biosensor surface by pulsed native chemical ligation.

Chembiochem, 8, 1790-1794.

17060469

J.K.Sabo, D.W.Keizer, Z.P.Feng, J.L.Casey, K.Parisi, A.M.Coley, M.Foley, and R.S.Norton (2007).
Mimotopes of apical membrane antigen 1: Structures of phage-derived peptides recognized by the inhibitory monoclonal antibody 4G2dc1 and design of a more active analogue.

Infect Immun, 75, 61-73.

17264074

R.E.Herman, D.Badders, M.Fuller, E.G.Makienko, M.E.Houston, S.C.Quay, and P.H.Johnson (2007).
The Trp cage motif as a scaffold for the display of a randomized peptide library on bacteriophage T7.

J Biol Chem, 282, 9813-9824.

16600968

J.J.Rice, A.Schohn, P.H.Bessette, K.T.Boulware, and P.S.Daugherty (2006).
Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands.

Protein Sci, 15, 825-836.

16233816

F.Uchiyama, Y.Tanaka, Y.Minari, and N.Tokui (2005).
Designing scaffolds of peptides for phage display libraries.

J Biosci Bioeng, 99, 448-456.

16155946

T.A.Naumann, S.N.Savinov, and S.J.Benkovic (2005).
Engineering an affinity tag for genetically encoded cyclic peptides.

Biotechnol Bioeng, 92, 820-830.

12021449

D.Legendre, B.Vucic, V.Hougardy, A.L.Girboux, C.Henrioul, J.Van Haute, P.Soumillion, and J.Fastrez (2002).
TEM-1 beta-lactamase as a scaffold for protein recognition and assay.

Protein Sci, 11, 1506-1518.

11910031

I.P.Korndörfer, and A.Skerra (2002).
Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site.

Protein Sci, 11, 883-893.

PDB codes:

1kff 1kl3 1kl4 1kl5

11933066

T.Lazaridis, A.Masunov, and F.Gandolfo (2002).
Contributions to the binding free energy of ligands to avidin and streptavidin.

Proteins, 47, 194-208.

11445463

D.J.Christensen, E.B.Gottlin, R.E.Benson, and P.T.Hamilton (2001).
Phage display for target-based antibacterial drug discovery.

Drug Discov Today, 6, 721-727.

11371463

D.Jain, K.J.Kaur, and D.M.Salunke (2001).
Plasticity in protein-peptide recognition: crystal structures of two different peptides bound to concanavalin A.

Biophys J, 80, 2912-2921.

PDB codes:

1jui 1jyc

11345431

G.A.Soukup, E.C.DeRose, M.Koizumi, and R.R.Breaker (2001).
Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes.

RNA, 7, 524-536.

11456486

N.J.Skelton, Y.M.Chen, N.Dubree, C.Quan, D.Y.Jackson, A.Cochran, K.Zobel, K.Deshayes, M.Baca, M.T.Pisabarro, and H.B.Lowman (2001).
Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1.

Biochemistry, 40, 8487-8498.

PDB codes:

1gje 1gjf 1gjg 1imw 1in2 1in3

11551471

R.C.Ladner, and A.C.Ley (2001).
Novel frameworks as a source of high-affinity ligands.

Curr Opin Biotechnol, 12, 406-410.

11259313

T.Coussaert, A.R.Völkel, J.Noolandi, and A.P.Gast (2001).
Streptavidin tetramerization and 2D crystallization: a mean-field approach.

Biophys J, 80, 2004-2010.

10851196

G.A.Soukup, and R.R.Breaker (2000).
Allosteric nucleic acid catalysts.

Curr Opin Struct Biol, 10, 318-325.

10861378

P.K.Pallaghy, and R.S.Norton (2000).
The cyclic contryphan motif CPxXPXC, a robust scaffold potentially useful as an omega-conotoxin mimic.

Biopolymers, 54, 173-179.

PDB code:

1d7t

10713989

U.Samanta, D.Pal, and P.Chakrabarti (2000).
Environment of tryptophan side chains in proteins.

Proteins, 38, 288-300.

10611647

G.M.Verkhivker, P.A.Rejto, D.Bouzida, S.Arthurs, A.B.Colson, S.T.Freer, D.K.Gehlhaar, V.Larson, B.A.Luty, T.Marrone, and P.W.Rose (1999).
Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.

J Mol Recognit, 12, 371-389.

9819200

D.S.Sem, B.L.Baker, E.J.Victoria, D.S.Jones, D.Marquis, L.Yu, J.Parks, and S.M.Coutts (1998).
Structural characterization and optimization of antibody-selected phage library mimotopes of an antigen associated with autoimmune recurrent thrombosis.

Biochemistry, 37, 16069-16081.

9862799

M.N.Rozinov, and G.P.Nolan (1998).
Evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores.

Chem Biol, 5, 713-728.

9148939

B.A.Katz, and R.T.Cass (1997).
In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0.

J Biol Chem, 272, 13220-13228.

PDB codes:

1vwa 1vwb 1vwc 1vwd 1vwe 1vwf 1vwg 1vwh 1vwi 1vwj 1vwk 1vwl 1vwm 1vwn 1vwo 1vwp 1vwq 1vwr

9241412

B.A.Katz (1997).
Structural and mechanistic determinants of affinity and specificity of ligands discovered or engineered by phage display.

Annu Rev Biophys Biomol Struct, 26, 27-45.

9241425

H.B.Lowman (1997).
Bacteriophage display and discovery of peptide leads for drug development.

Annu Rev Biophys Biomol Struct, 26, 401-424.

9194176

S.Freitag, I.Le Trong, L.Klumb, P.S.Stayton, and R.E.Stenkamp (1997).
Structural studies of the streptavidin binding loop.

Protein Sci, 6, 1157-1166.

PDB codes:

1swa 1swb 1swc 1swd 1swe

9230477

S.Ostergaard, and A.Holm (1997).
Synthesis and screening of an indexed motif-library containing non-proteinogenic amino acids.

J Pept Sci, 3, 123-132.

8951652

A.N.Jain (1996).
Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities.

J Comput Aided Mol Des, 10, 427-440.

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.