1B2I

KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID (AMCHA) COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY, RAMACHANDRAN PLOT, LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution structure and dynamics of the plasminogen kringle 2-AMCHA complex: 3(1)-helix in homologous domains.

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

(1999) Biochemistry 38: 15741-15755


  • PubMed Abstract: 
  • The kringle 2 (K2) module of human plasminogen (Pgn) binds L-lysine and analogous zwitterionic compounds, such as the antifibronolytic agent trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA). Far-UV CD and NMR spectra reveal little conformational ...

    The kringle 2 (K2) module of human plasminogen (Pgn) binds L-lysine and analogous zwitterionic compounds, such as the antifibronolytic agent trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA). Far-UV CD and NMR spectra reveal little conformational change in K2 upon ligand binding. However, retarded (1)H-(2)H isotope exchange kinetics induced by AMCHA indicate stabilization of the K2 conformation by the ligand. Assessment of secondary structure content from CD spectra yields approximately 26% beta-STRAND, approximately 13% beta-TURN, approximately 15% 3(1)-HELIX, and approximately 6% 3(10)-HELIX. The NMR solution conformation of the K2 domain complexed to AMCHA has been determined [heavy atom rmsd = 0.49 +/- 0.09A (BACKBONE) AND 1.02+/- 0.08 (ALL)]. The K2 molecule has overall dimensions of approximately 34.5A times approximately 33.4A times approximately 22.7A . Analogous with the polypeptide outline of homologous domains, K2 contains three short antiparallel beta-sheets (paired strands 15-16/20-21, 24-25/48-49, and 62-64/72-74) and four defined beta-turns (residues 6-9, 16-19, 53-56, AND 67-70). Consistent with the CD analysis, albeit novel in the context of kringle folding, the NMR structure reveals an unpaired beta-strand structured by residues 30-32, a turn of 3(10)-helix compromising residues 38-41, and a 3(1)-helix for residues 21-24 and 74-79. We also identify alignable 3(1)-helices in previously reported homologous kringle structures. Rather high order parameter S(2) values (= approximately 0.85 +/- 0.04) characterize the K2 backbone dynamics. The lowest flexibility is observed for the two inner loop segments of residues 51-63 AND 63-75 (= approximately 0.86-0.87 +/- 0.03). Overhauser connectivities reveal close hydrophobic contacts of the ligand ring with side chains of Tyr(36), Trp(62), Phe(64), Trp(72), AND Leu(74). In most K2 structures, the N atom of AMCHA places itself approximately 3.9 and 4.4A from the anionic groups of Glu(57) and Asp(55), respectively, while its carboxylate group, H-bonded to the Tyr(36) side chain OH(eta), ion-pairs the Arg(71) guanidinium group. Consistent with the preference of K2 for binding 5-aminopentanoic acid over 6-aminohexanoic acid, the positions of the ionic centers within the K2 binding site approach each other approximately 1A closer relative to what is observed in lysine binding sites of homologous Pgn modules.


    Related Citations: 
    • Expression, Purification and Characterization of the Recombinant Kringle 2 and Kringle 3 Domains of Human Plasminogen and Analysis of Their Binding Affinity for Omega-Aminocarboxylic Acids
      Marti, D.,Schaller, J.,Ochensberger, B.,Rickli, E.E.
      (1994) Eur.J.Biochem. 219: 455
    • Recombinant Gene Expression and 1H NMR Characteristics of the Kringle (2+3) Supermodule: Spectroscopic/Functional Individuality of Plasminogen Kringle Domains
      Soehndel, S.,Hu, C.K.,Marti, D.,Affolter, M.,Schaller, J.,Llinas, M.,Rickli, E.E.
      (1996) Biochemistry 35: 2357
    • Ligand Preferences of Kringle 2 and Homologous Domains of Human Plasminogen: Canvassing Weak, Intermediate and High-Affinity Binding Sites by 1H-NMR
      Marti, D.N.,Hu, C.K.,An, S.S.A.,Von Haller, P.,Schaller, J.,Llinas, M.
      (1997) Biochemistry 36: 11591


    Organizational Affiliation

    Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PLASMINOGEN)
A
83Homo sapiensMutation(s): 3 
Gene Names: PLG
EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens)
Go to Gene View: PLG
Go to UniProtKB:  P00747
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMH
Query on AMH

Download SDF File 
Download CCD File 
A
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID
C8 H15 N O2
GYDJEQRTZSCIOI-LJGSYFOKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY, RAMACHANDRAN PLOT, LEAST RESTRAINT VIOLATION 
  • Olderado: 1B2I Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations