1I71

HIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV TYPE 7: INSIGHTS INTO LIGAND BINDING

Summary for 1I71

• Entry DOI: 10.2210/pdb1i71/pdb
• Descriptor: APOLIPOPROTEIN(A), SULFATE ION (3 entities in total)
• Functional Keywords: alipoprotein(a), kringle, protein-ligand interaction, lysine binding, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 9874.81

Authors

Ye, Q.,Rahman, M.N.,Koschinsky, M.L.,Jia, Z. (deposition date: 2001-03-07, release date: 2001-06-13, Last modification date: 2023-08-09)

Primary citation

Ye, Q.,Rahman, M.N.,Koschinsky, M.L.,Jia, Z.
High-resolution crystal structure of apolipoprotein(a) kringle IV type 7: insights into ligand binding.
Protein Sci., 10:1124-1129, 2001

PubMed Abstract: Apolipoprotein(a) [apo(a)] consists of a series of tandemly repeated modules known as kringles that are commonly found in many proteins involved in the fibrinolytic and coagulation cascades, such as plasminogen and thrombin, respectively. Specifically, apo(a) contains multiple tandem repeats of domains similar to plasminogen kringle IV (designated as KIV(1) to KIV(10)) followed by sequences similar to the kringle V and protease domains of plasminogen. The KIV domains of apo(a) differ with respect to their ability to bind lysine or lysine analogs. KIV(10) represents the high-affinity lysine-binding site (LBS) of apo(a); a weak LBS is predicted in each of KIV(5)-KIV(8) and has been directly demonstrated in KIV(7). The present study describes the first crystal structure of apo(a) KIV(7), refined to a resolution of 1.45 A, representing the highest resolution for a kringle structure determined to date. A critical substitution of Tyr-62 in KIV(7) for the corresponding Phe-62 residue in KIV(10), in conjunction with the presence of Arg-35 in KIV(7), results in the formation of a unique network of hydrogen bonds and electrostatic interactions between key LBS residues (Arg-35, Tyr-62, Asp-54) and a peripheral tyrosine residue (Tyr-40). These interactions restrain the flexibility of key LBS residues (Arg-35, Asp-54) and, in turn, reduce their adaptability in accommodating lysine and its analogs. Steric hindrance involving Tyr-62, as well as the elimination of critical ligand-stabilizing interactions within the LBS are also consequences of this interaction network. Thus, these subtle yet critical structural features are responsible for the weak lysine-binding affinity exhibited by KIV(7) relative to that of KIV(10).

PubMed: 11369850
DOI: 10.1110/ps.01701

Experimental method

X-RAY DIFFRACTION (1.45 Å)