1WHT

STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0-A resolution.

Bullock, T.L.Branchaud, B.Remington, S.J.

(1994) Biochemistry 33: 11127-11134

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the complex of L-benzylsuccinate (Ki = 0.2 mM) bound to wheat serine carboxypeptidase II has been analyzed at 2.0-A resolution for native and inhibited crystals at -170 degrees C. The model has been refined and has a standard crystal ...

    The structure of the complex of L-benzylsuccinate (Ki = 0.2 mM) bound to wheat serine carboxypeptidase II has been analyzed at 2.0-A resolution for native and inhibited crystals at -170 degrees C. The model has been refined and has a standard crystallographic R-factor of 0.176 for 57,734 reflections observed between 20.0- and 2.0-A resolution. The root mean square deviation from ideal bonds is 0.017 A and from ideal angles is 2.6 degrees. The model consists of 400 amino acids, 4 N-linked saccharide residues, and 430 water molecules. L-Benzylsuccinate occupies a narrow slot in the active site defined by Tyr 60, Tyr 239, and the polypeptide backbone. One carboxylate forms hydrogen bonds to Glu 145, Asn 51, the amide of Gly 52, and the catalytic His 397, suggestive of how the peptide C-terminal carboxylate is recognized by the enzyme. The phenyl ring stacks between Tyr 239 and Tyr 60, while the other carboxylate occupies the "oxyanion hole". One of the oxygens accepts hydrogen bonds from the amides of Tyr 147 and Gly 53, while the other forms a very close contact (2.3 A) with the O gamma of Ser 146, forcing the side chain into a conformation alternative to that found in the resting state of the enzyme. The inhibitor occupies the active site in a way that suggests that it can be regarded as a transition-state analogue of serine carboxypeptidases. The model suggests a novel enzymatic mechanism, involving substrate-assisted catalysis, that might account for the low pH optimum (4.0-5.5) of peptidase activity unique to this family of serine proteinases.


    Related Citations: 
    • Primary Structure and Enzymatic Properties of Carboxypeptidase II from Wheat Bran
      Breddam, K.,Sorensen, S.B.,Svendsen, I.
      (1987) Carlsberg Res.Commun. 52: 297
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE CARBOXYPEPTIDASE II
A
256Triticum 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
B
153Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
Find proteins for P08819 (Triticum aestivum)
Go to UniProtKB:  P08819
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

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

Download SDF File 
Download CCD File 
A
L-BENZYLSUCCINIC ACID
C11 H12 O4
GTOFKXZQQDSVFH-SECBINFHSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZSKi: 200000 nM BINDINGMOAD
BZSKi: 200000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.500α = 90.00
b = 95.500β = 90.00
c = 208.600γ = 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: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other