PDBsum entry: 1b2i

Hydrolase

PDB-id: 1b2i

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

83 a.a. *

Ligands

AMH

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1b2i

Name:

Hydrolase

Title:

Kringle 2 domain of human plasminogen: nmr solution structure of trans-4-aminomethylcyclohexane-1-carboxylic acid (amcha) complex

Structure:

Protein (plasminogen). Chain: a. Fragment: kringle 2 domain. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

UniProt:

P00747 (PLMN_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

810 a.a.

Struc:

83 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* 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:

D.N.Marti,J.Schaller,M.Llinas

Key ref:

J.R.Tame et al. (1995). The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.. Structure, 3, 1395-1406. [PubMed id: 8747465] [DOI: 10.1016/S0969-2126(01)00276-3]

Date:

24-Sep-99

Release date:

19-Nov-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(01)00276-3

Structure 3:1395-1406 (1995)

PubMed id: 8747465

The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.

J.R.Tame, E.J.Dodson, G.Murshudov, C.F.Higgins, A.J.Wilkinson.

ABSTRACT

BACKGROUND: The periplasmic oligopeptide-binding protein OppA has a remarkably broad substrate specificity, binding peptides of two or five amino-acid residues with high affinity, but little regard to sequence. It is therefore an ideal system for studying how different chemical groups can be accommodated in a protein interior. The ability of the protein to bind peptides of different lengths has been studied by co-crystallising it with different ligands. RESULTS: Crystals of OppA from Salmonella typhimurium complexed with the peptides Lys-Lys-Lys (KKK) and Lys-Lys-Lys-Ala (KKKA) have been grown in the presence of uranyl ions which form important crystal contacts. These structures have been refined to 1.4 A and 2.1 A, respectively. The ligands are completely enclosed, their side chains pointing into large hydrated cavities and making few strong interactions with the protein. CONCLUSIONS: Tight peptide binding by OppA arises from strong hydrogen bonding and electrostatic interactions between the protein and the main chain of the ligand. Different basic side chains on the protein form salt bridges with the C terminus of peptide ligands of different lengths.

Selected figure(s)

Figure 1.
Figure 1. Stereo Cα trace of OppA in the closed, ligand bound form. The tri-lysine ligand is shown in thicker lines. Figure 1. Stereo Cα trace of OppA in the closed, ligand bound form. The tri-lysine ligand is shown in thicker lines.

Figure 5.
Figure 5. . Schematic diagram illustrating the interactions made by the main chain of the tri-lysine ligand with OppA. Protein residues are labelled. Hydrogen bonding and electrostatic interactions are indicated by the dotted lines. R1, R2 and R3 indicate the ligand side chains. Figure 5. . Schematic diagram illustrating the interactions made by the main chain of the tri-lysine ligand with OppA. Protein residues are labelled. Hydrogen bonding and electrostatic interactions are indicated by the dotted lines. R1, R2 and R3 indicate the ligand side chains.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1395-1406) copyright 1995.

Figures were selected by an automated process.