1BCR

COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, ANTIPAIN, AND ARGININE AT ROOM TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity.

Bullock, T.L.Breddam, K.Remington, S.J.

(1996) J.Mol.Biol. 255: 714-725

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of two ternary complexes of wheat serine carboxypeptidase II (CPD-WII), with a tetrapeptide aldehyde and a reaction product arginine, have been determined by X-ray crystallography at room temperature and -170 degrees. The peptide aldeh ...

    The structures of two ternary complexes of wheat serine carboxypeptidase II (CPD-WII), with a tetrapeptide aldehyde and a reaction product arginine, have been determined by X-ray crystallography at room temperature and -170 degrees. The peptide aldehydes, antipain and chymostatin, form covalent adducts with the active-site serine 146. The CPD-WII antipain arginine model has a standard crystallographic R-factor of 0.162, with good geometry at 2.5 A resolution for data collected at room temperature. The -170 degrees C model of the chymostatin arginine complex has an R-factor of 0.174, with good geometry using data to 2.1 A resolution. The structures suggest binding subsites N-terminal to the scissile bond. All four residues of chymostatin are well-localized in the putative S1 through S4 sites, while density is apparent only in S1 and S2 for antipain. In the S1 site, Val340 and 341, Phe215 and Leu216 form a hydrophobic binding surface, not a pocket, for the P1 phenylalanyl side-chain of chymostatin. The P1 arginyl of antipain also binds at this site, but the positive charge appears to be stabilized by additional solvent molecules. Thus, the hybrid nature of the S1 site accounts for the ability of CPD-WII to accept both hydrophobic and basic residues at P1. Hydrogen bonds to the peptide substrate backbone are few and are made primarily with side-chains on the enzyme. Thus, substrate recognition by CPD-WII appears to have nothing in common with that of the other families of serine proteinases. The hemiacetal linkages to the essential Ser146 are of a single stereoisomer with tetrahedral geometry, with an oxygen atom occupying the "oxyanion hole" region of the enzyme. This atom accepts three hydrogen bonds, two from the polypeptide backbone and one from the positively-charged amino group of bound arginine, and must be negatively charged. Thus, the combination of ligands forms an excellent approximation to the oxyanion intermediate formed during peptide hydrolysis. Surprisingly, the (R) stereochemistry at the hemiacetal linkage is opposite to that expected by comparison to previously determined structures of peptide aldehydes complexed with Streptomyces griseus proteinase A. This is shown to be a consequence of the approximate mirror symmetry of the arrangement of catalytic groups in the two families of serine proteases and suggests that the stereochemical course of the two enzymatic reactions differ in handedness.


    Related Citations: 
    • Refined Atomic Model of Wheat Serine Carboxypeptidase II at 2.2 Angstrom Resolution
      Liao, D.I.,Breddam, K.,Sweet, R.M.,Bullock, T.,Remington, S.J.
      (1992) Biochemistry 31: 9796
    • Structure of the Complex of L-Benzylsuccinate with Wheat Serine Carboxypeptidase at 2.0 Angstrom Resolution
      Bullock, T.L.,Branchaud, B.,Remington, S.J.
      (1994) Biochemistry 33: 11127


    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
263Triticum 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
160Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
Find proteins for P08819 (Triticum aestivum)
Go to UniProtKB:  P08819
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTIPAIN
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 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
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000180
Query on PRD_000180
CAntipainOligopeptide / Enzyme inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 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
R-AXISdata collection
R-AXISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    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: 2011-12-28
    Type: Non-polymer description, Structure summary
  • Version 1.4: 2012-09-05
    Type: Derived calculations
  • Version 1.5: 2012-12-12
    Type: Other
  • Version 1.6: 2013-06-05
    Type: Atomic model