PDBsum entry: 2knf

Blood clotting

PDB-id: 2knf

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

86 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2knf

Name:

Blood clotting

Title:

Solution structure and functional characterization of human plasminogen kringle 5

Structure:

Plasminogen. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plg. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Expression_system_variant: (met+)

UniProt:

P00747 (PLMN_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

810 a.a.

Struc:

86 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

E.C.3.4.21.7   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.

Resolution:

not givenÅ

NMR structure:

20 models

Authors:

M.D.Battistel,A.Grishaev,S.A.An,F.J.Castellino,M.Llinas

Key ref:

M.D.Battistel et al. (2009). Solution structure and functional characterization of human plasminogen kringle 5.. Biochemistry, 48, 10208-10219. [PubMed id: 19821587] [DOI: 10.1021/bi901433n]

Date:

21-Aug-09

Release date:

27-Oct-09

Related entries:

16466 related db: bmrb

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1021/bi901433n

Biochemistry 48:10208-10219 (2009)

PubMed id: 19821587

Solution structure and functional characterization of human plasminogen kringle 5.

M.D.Battistel, A.Grishaev, S.S.An, F.J.Castellino, M.Llinás.

ABSTRACT

The ligand binding properties of the kringle 5 (K5) domain of human plasminogen have been investigated via intrinsic tryptophan fluorescence. The oleic acid (OA) affinity for K5 was quantified, yielding an association constant K(a) approximately 2.08 x 10(4) mM(-1). Simultaneously, it was determined that OA and trans-4-(aminomethyl)cyclohexanecarboxylic acid (AMCHA) (K(a) approximately 50 mM(-1)) compete for binding to K5. The solution structure of K5 in the presence of 11 mM AMCHA was solved via NMR spectroscopy (protein heavy atom RMSD approximately 0.93 +/- 0.12 A). The AMCHA binding site was localized via (1)H/(15)N chemical shift perturbation mapping assisted by in silico docking. We have found that AMCHA binds at the canonical kringle lysine binding site (LBS), structured by the Pro54-Gly60 segment plus the neighboring Phe36, Thr37, Trp62, Leu71, and Tyr72 residues. The segment 30-42, encompassing LBS residues, appears to be endowed with a higher degree of structural flexibility as suggested by the relatively lower value of S(2), the generalized order parameter, consistent with a higher backbone heavy atom RMSD of approximately 1.22 A (vs 0.84 A overall) between the two monomeric units in the crystal unit cell, of potential significance for ligand binding. OA was found to perturb the same area of the protein, namely, the LBS, as well as Tyr74. Combined with previous studies, the observation of OA binding expands the range of ligands that interact with kringle 5 while it widens the scope of potential biological functions for kringle domains.