3SC2

REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution.

Liao, D.I.Breddam, K.Sweet, R.M.Bullock, T.Remington, S.J.

(1992) Biochemistry 31: 9796-9812


  • PubMed Abstract: 
  • The crystal structure of the homodimeric serine carboxypeptidase II from wheat (CPDW-II, M(r) 120K) has been determined and fully refined at 2.2-A resolution to a standard crystallographic R factor of 16.9% using synchrotron data collected at the Bro ...

    The crystal structure of the homodimeric serine carboxypeptidase II from wheat (CPDW-II, M(r) 120K) has been determined and fully refined at 2.2-A resolution to a standard crystallographic R factor of 16.9% using synchrotron data collected at the Brookhaven National Laboratory. The model has an rms deviation from ideal bond lengths of 0.018 A and from bond angles of 2.8 degrees. The model supports the general conclusions of an earlier study at 3.5-A resolution and will form the basis for investigation into substrate binding and mechanistic studies. The enzyme has an alpha + beta fold, consisting of a central 11-stranded beta-sheet with a total of 15 helices on either side. The enzyme, like other serine proteinases, contains a "catalytic triad" Ser146-His397-Asp338 and a presumed "oxyanion hole" consisting of the backbone amides of Tyr147 and Gly53. The carboxylate of Asp338 and imidazole of His397 are not coplanar in contrast to the other serine proteinases. A comparison of the active site features of the three families of serine proteinases suggests that the "catalytic triad" should actually be regarded as two diads, a His-Asp diad and a His-Ser diad, and that the relative orientation of one diad with respect to the other is not particularly important. Four active site residues (52, 53, 65, and 146) have unfavorable backbone conformations but have well-defined electron density, suggesting that there is some strain in the active site region. The binding of the free amino acid arginine has been analyzed by difference Fourier methods, locating the binding site for the C-terminal carboxylate of the leaving group. The carboxylate makes hydrogen bonds to Glu145, Asn51, and the amide of Gly52. The carboxylate of Glu145 also makes a hydrogen bond with that of Glu65, suggesting that one or both may be protonated. Thus, the loss of peptidase activity at pH > 7 may in part be due to deprotonation of Glu145. The active site does not reveal exposed peptide amides and carbonyl oxygen atoms that could interact with substrate in an extended beta-sheet fashion. The fold of the polypeptide backbone is completely different than that of trypsin or subtilisin, suggesting that this is a third example of convergent molecular evolution to a common enzymatic activity. Furthermore, it is suggested that the active site sequence motif "G-X-S-X-G/A", often considered the hallmark of serine peptidase or esterase activity, is fortuitous and not the result of divergent evolution.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Structure of Wheat Serine Carboxypeptidase II at 3.5 Angstroms Resolution
      Liao, D.-I.,Remington, S.J.
      (1990) J.Biol.Chem. 265: 6528
    • Crystallization of Serine Carboxypeptidases
      Wilson, K.P.,Liao, D.-I.,Bullock, T.,Remington, S.J.,Breddam, K.
      (1990) J.Mol.Biol. 211: 301
    • Primary Structure and Enzymatic Properties of Carboxypeptidase II from Wheat Bran
      Breddam, K.,Sorensen, S.B.,Svendsen, I.
      (1987) Carlsberg Res.Commun. 52: 297


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE CARBOXYPEPTIDASE II (CPDW-II)
A
259Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
Find proteins for P08819 (Triticum aestivum)
Go to UniProtKB:  P08819
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SERINE CARBOXYPEPTIDASE II (CPDW-II)
B
152Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
Find proteins for P08819 (Triticum aestivum)
Go to UniProtKB:  P08819
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.400α = 90.00
b = 98.400β = 90.00
c = 209.500γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other