PDBsum entry 1v6d

Hydrolase

PDB id

1v6d

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Contents

			Protein chain

					223 a.a. *

			Ligands

					PRO-ASP-AIB-LEU- AIB-LEU-ALA


					ACT


					TBF


					NME

			Metals

					_CA

			Waters ×160

* Residue conservation analysis

PDB id:

1v6d

Links
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Name:

Hydrolase

Title:

The crystal structure of the trypsin complex with synthetic heterochiral peptide

Structure:

Trypsin. Chain: a. Pd(aib)l(aib)la. Chain: b. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Synthetic: yes. Other_details: a heterochiral heptapeptide synthesized chemically.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å

R-factor:

0.155

R-free:

0.178

Authors:

N.Shamaladevi,V.Pattabhi

Key ref:

N.Shamaladevi and V.Pattabhi (2005). Secondary binding site of trypsin: revealed by crystal structure of trypsin-peptide complex. J Biomol Struct Dyn, 22, 635-642. PubMed id: 15842169

Date:

28-Nov-03

Release date:

07-Dec-04

PROCHECK

	Headers

	References

Protein chain

P00761 (TRYP_PIG) - Trypsin from Sus scrofa

Seq: Struc:					231 a.a. 223 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.4.21.4 - trypsin.

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

Reaction:

Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

	J Biomol Struct Dyn 22:635-642 (2005)
PubMed id: 15842169

Secondary binding site of trypsin: revealed by crystal structure of trypsin-peptide complex.
N.Shamaladevi, V.Pattabhi.

ABSTRACT

Designed synthetic heterochiral peptides, when added to porcine trypsin, resulted in reduction of enzyme activity. The crystal structure of a complex formed between porcine trypsin and a heterochiral hepta peptide Boc-Pro-DAsp-Aib-Leu-Aib-Leu-Ala-NHMe has been determined at 1.9 A resolution. The hepta peptide does not bind at the active site, but is located in the interstitial region, and interacts with the calcium-binding loop (residues 60-80). The bound peptide interacts with the active site residue Ser195 through an acetate ion, and with Lys 60 mediated by water molecules. The structure, when compared with the other trypsin-peptide complexes, suggests that the flexibility of surface loops, concerted movement of the loops towards the active site, and the interaction of the bound peptide with Lys 60, may be responsible for the reduction in enzyme activity. This study provides a structural evidence for the earlier biochemical observation regarding the role of surface loops in the catalysis of the enzyme.

Literature references that cite this PDB file's key reference

PubMed id

Reference

17372355

M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.

Acta Crystallogr D Biol Crystallogr, 63, 500-507.

PDB code:

2ayw

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 code is shown on the right.