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: 2.50 Å
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 3.0 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

  • DOI: 10.1006/jmbi.1996.0058
  • Primary Citation of Related Structures:  
    1BCR, 1BCS

  • 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 aldehydes, antipain and chymostatin, form covalent adducts with the active-site serine 146 ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE CARBOXYPEPTIDASE IIA263Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
UniProt
Find proteins for P08819 (Triticum aestivum)
Explore P08819 
Go to UniProtKB:  P08819
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE CARBOXYPEPTIDASE IIB160Triticum aestivumMutation(s): 0 
Gene Names: CBP2
EC: 3.4.16.6
UniProt
Find proteins for P08819 (Triticum aestivum)
Explore P08819 
Go to UniProtKB:  P08819
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIPAINC4ActinomycetiaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseD3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ARG (Subject of Investigation/LOI)
Query on ARG

Download Ideal Coordinates CCD File 
G [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OAR
Query on OAR
CPEPTIDE-LIKEC6 H16 N4 OARG
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000180
Query on PRD_000180
CAntipainOligopeptide /  Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.4α = 90
b = 98.4β = 90
c = 209.5γ = 90
Software Package:
Software NamePurpose
R-AXISdata collection
TNTrefinement
R-AXISdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Non-polymer description, Structure summary
  • Version 1.4: 2012-09-05
    Changes: Derived calculations
  • Version 1.5: 2012-12-12
    Changes: Other
  • Version 1.6: 2013-06-05
    Changes: Atomic model
  • Version 2.0: 2019-05-15
    Changes: Advisory, Data collection, Derived calculations, Other, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary