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Thrombin a-chain: activation remnant or allosteric effector?

Carter IS, Vanden Hoek AL, Pryzdial EL, Macgillivray RT - Thrombosis (2010)

Bottom Line: This paper summarizes the current data on the prothrombin catalytic domain A-chain region and the subsequent thrombin A-chain.Attention is given to biochemical characterization of naturally occurring prothrombin A-chain mutations and alanine scanning mutants in this region.While originally considered to be simply an activation remnant with little physiologic function, the thrombin A-chain is now thought to play a role as an allosteric effector in enzymatic reactions and may also be a structural scaffold to stabilize the protease domain.

View Article: PubMed Central - PubMed

Affiliation: Centre for Blood Research, University of British Columbia (UBC), Vancouver, BC, Canada V6T 1Z3.

ABSTRACT
Although prothrombin is one of the most widely studied enzymes in biology, the role of the thrombin A-chain has been neglected in comparison to the other domains. This paper summarizes the current data on the prothrombin catalytic domain A-chain region and the subsequent thrombin A-chain. Attention is given to biochemical characterization of naturally occurring prothrombin A-chain mutations and alanine scanning mutants in this region. While originally considered to be simply an activation remnant with little physiologic function, the thrombin A-chain is now thought to play a role as an allosteric effector in enzymatic reactions and may also be a structural scaffold to stabilize the protease domain.

No MeSH data available.


Related in: MedlinePlus

Pymol-generated structure of thrombin using the PDB 3GIS coordinates of Ser195Ala thrombin [8]. (a) Interactions between the A-chain and the B-chain of thrombin (B-chain residues are labeled in blue, the 36-amino acid residue A-chain is colored in green, and the covalently bound A13 peptide segment is colored magenta. The covalent disulfide bridge between the A- and B-chains is through Cys1(93)-Cys122, as shown in orange. Hydrogen bonds are colored yellow and residue numbering is based on chymotrypsinogen, with prothrombin numbering for the A-chain provided in brackets. The A-chain is stabilized by the Asp1a(92)-Lys9(301) and Arg14d(310)-Glu13(314) ion pairs and the ion quartet Arg4(96)-Glu8(300)-Asp14(306)-Glu14c(309). The ionic interactions include Glu8(300)-Lys202-Glu14c(309), Asp14(306)-Arg137, Lys14a(307)-Glu23, and Glu14e(311)-Lys135-Asn159-Tyr194a. Hydrophobic stacking interactions include Tyr14j(316)-Pro204 and Phe1m(280)-Phe1l(281)-Phe1g(286) in the A13 peptide of the A-chain. (b) Thrombin structure showing active site residues in red and location of the A-chain on the opposite face of the molecule.
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fig2: Pymol-generated structure of thrombin using the PDB 3GIS coordinates of Ser195Ala thrombin [8]. (a) Interactions between the A-chain and the B-chain of thrombin (B-chain residues are labeled in blue, the 36-amino acid residue A-chain is colored in green, and the covalently bound A13 peptide segment is colored magenta. The covalent disulfide bridge between the A- and B-chains is through Cys1(93)-Cys122, as shown in orange. Hydrogen bonds are colored yellow and residue numbering is based on chymotrypsinogen, with prothrombin numbering for the A-chain provided in brackets. The A-chain is stabilized by the Asp1a(92)-Lys9(301) and Arg14d(310)-Glu13(314) ion pairs and the ion quartet Arg4(96)-Glu8(300)-Asp14(306)-Glu14c(309). The ionic interactions include Glu8(300)-Lys202-Glu14c(309), Asp14(306)-Arg137, Lys14a(307)-Glu23, and Glu14e(311)-Lys135-Asn159-Tyr194a. Hydrophobic stacking interactions include Tyr14j(316)-Pro204 and Phe1m(280)-Phe1l(281)-Phe1g(286) in the A13 peptide of the A-chain. (b) Thrombin structure showing active site residues in red and location of the A-chain on the opposite face of the molecule.

Mentions: As shown in Figure 2, the A-chain of thrombin extends along the surface of the B-chain in a shallow curved groove, arranged in a boomerang-like shape opposite the active site [6]. X-ray crystallography structures of human thrombin show that the A-chain hinges the two interacting six-stranded beta barrels of the B-chain. The A-chain interacts with the B-chain through a network of six buried salt bridges and ionic interactions, and ten interchain H-bonds that stabilize the orientation of the B domain barrels. The A-chain is further stabilized through several intramolecular polar and salt bridge interactions [7]. The central portion of the A-chain is most rigid, due to the presence of strong salt bridge interactions (Figure 2). The X-ray crystal structure of thrombin also reveals that both termini of the A-chain are disordered, raising the question: “How much of the A-chain is required to maintain thrombin stability and activity?” The C-terminal segment up to Tyr14j is an amphiphilic alpha-helix forming one and a half turns, showing a high degree of flexibility as well [6]. The N-terminal sequence of the A-chain up to residue Glu1c is characterized by weak electron density and appears to have a high degree of conformational flexibility. This suggests that this sequence does not interact strongly with other parts of the thrombin molecule and may not contribute significantly to the overall structural stability of the enzyme. However, there have been no studies conducted to exclude other biological functions.


Thrombin a-chain: activation remnant or allosteric effector?

Carter IS, Vanden Hoek AL, Pryzdial EL, Macgillivray RT - Thrombosis (2010)

Pymol-generated structure of thrombin using the PDB 3GIS coordinates of Ser195Ala thrombin [8]. (a) Interactions between the A-chain and the B-chain of thrombin (B-chain residues are labeled in blue, the 36-amino acid residue A-chain is colored in green, and the covalently bound A13 peptide segment is colored magenta. The covalent disulfide bridge between the A- and B-chains is through Cys1(93)-Cys122, as shown in orange. Hydrogen bonds are colored yellow and residue numbering is based on chymotrypsinogen, with prothrombin numbering for the A-chain provided in brackets. The A-chain is stabilized by the Asp1a(92)-Lys9(301) and Arg14d(310)-Glu13(314) ion pairs and the ion quartet Arg4(96)-Glu8(300)-Asp14(306)-Glu14c(309). The ionic interactions include Glu8(300)-Lys202-Glu14c(309), Asp14(306)-Arg137, Lys14a(307)-Glu23, and Glu14e(311)-Lys135-Asn159-Tyr194a. Hydrophobic stacking interactions include Tyr14j(316)-Pro204 and Phe1m(280)-Phe1l(281)-Phe1g(286) in the A13 peptide of the A-chain. (b) Thrombin structure showing active site residues in red and location of the A-chain on the opposite face of the molecule.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3211113&req=5

fig2: Pymol-generated structure of thrombin using the PDB 3GIS coordinates of Ser195Ala thrombin [8]. (a) Interactions between the A-chain and the B-chain of thrombin (B-chain residues are labeled in blue, the 36-amino acid residue A-chain is colored in green, and the covalently bound A13 peptide segment is colored magenta. The covalent disulfide bridge between the A- and B-chains is through Cys1(93)-Cys122, as shown in orange. Hydrogen bonds are colored yellow and residue numbering is based on chymotrypsinogen, with prothrombin numbering for the A-chain provided in brackets. The A-chain is stabilized by the Asp1a(92)-Lys9(301) and Arg14d(310)-Glu13(314) ion pairs and the ion quartet Arg4(96)-Glu8(300)-Asp14(306)-Glu14c(309). The ionic interactions include Glu8(300)-Lys202-Glu14c(309), Asp14(306)-Arg137, Lys14a(307)-Glu23, and Glu14e(311)-Lys135-Asn159-Tyr194a. Hydrophobic stacking interactions include Tyr14j(316)-Pro204 and Phe1m(280)-Phe1l(281)-Phe1g(286) in the A13 peptide of the A-chain. (b) Thrombin structure showing active site residues in red and location of the A-chain on the opposite face of the molecule.
Mentions: As shown in Figure 2, the A-chain of thrombin extends along the surface of the B-chain in a shallow curved groove, arranged in a boomerang-like shape opposite the active site [6]. X-ray crystallography structures of human thrombin show that the A-chain hinges the two interacting six-stranded beta barrels of the B-chain. The A-chain interacts with the B-chain through a network of six buried salt bridges and ionic interactions, and ten interchain H-bonds that stabilize the orientation of the B domain barrels. The A-chain is further stabilized through several intramolecular polar and salt bridge interactions [7]. The central portion of the A-chain is most rigid, due to the presence of strong salt bridge interactions (Figure 2). The X-ray crystal structure of thrombin also reveals that both termini of the A-chain are disordered, raising the question: “How much of the A-chain is required to maintain thrombin stability and activity?” The C-terminal segment up to Tyr14j is an amphiphilic alpha-helix forming one and a half turns, showing a high degree of flexibility as well [6]. The N-terminal sequence of the A-chain up to residue Glu1c is characterized by weak electron density and appears to have a high degree of conformational flexibility. This suggests that this sequence does not interact strongly with other parts of the thrombin molecule and may not contribute significantly to the overall structural stability of the enzyme. However, there have been no studies conducted to exclude other biological functions.

Bottom Line: This paper summarizes the current data on the prothrombin catalytic domain A-chain region and the subsequent thrombin A-chain.Attention is given to biochemical characterization of naturally occurring prothrombin A-chain mutations and alanine scanning mutants in this region.While originally considered to be simply an activation remnant with little physiologic function, the thrombin A-chain is now thought to play a role as an allosteric effector in enzymatic reactions and may also be a structural scaffold to stabilize the protease domain.

View Article: PubMed Central - PubMed

Affiliation: Centre for Blood Research, University of British Columbia (UBC), Vancouver, BC, Canada V6T 1Z3.

ABSTRACT
Although prothrombin is one of the most widely studied enzymes in biology, the role of the thrombin A-chain has been neglected in comparison to the other domains. This paper summarizes the current data on the prothrombin catalytic domain A-chain region and the subsequent thrombin A-chain. Attention is given to biochemical characterization of naturally occurring prothrombin A-chain mutations and alanine scanning mutants in this region. While originally considered to be simply an activation remnant with little physiologic function, the thrombin A-chain is now thought to play a role as an allosteric effector in enzymatic reactions and may also be a structural scaffold to stabilize the protease domain.

No MeSH data available.


Related in: MedlinePlus