1CZC

ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH GLUTARIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cocrystallization of a mutant aspartate aminotransferase with a C5-dicarboxylic substrate analog: structural comparison with the enzyme-C4-dicarboxylic analog complex.

Oue, S.Okamoto, A.Yano, T.Kagamiyama, H.

(2000) J Biochem 127: 337-343

  • DOI: 10.1093/oxfordjournals.jbchem.a022612
  • Primary Citation of Related Structures:  
    1CZC, 1CZE

  • PubMed Abstract: 
  • A mutant Escherichia coil aspartate aminotransferase with 17 amino acid substitutions (ATB17), previously created by directed evolution, shows increased activity for beta-branched amino acids and decreased activity for the native substrates, aspartate and glutamate ...

    A mutant Escherichia coil aspartate aminotransferase with 17 amino acid substitutions (ATB17), previously created by directed evolution, shows increased activity for beta-branched amino acids and decreased activity for the native substrates, aspartate and glutamate. A new mutant (ATBSN) was generated by changing two of the 17 mutated residues back to the original ones. ATBSN recovered the activities for aspartate and glutamate to the level of the wild-type enzyme while maintaining the enhanced activity of ATB17 for the other amino acid substrates. The absorption spectrum of the bound coenzyme, pyridoxal 5'-phosphate, also returned to the original state. ATBSN shows significantly increased affinity for substrate analogs including succinate and glutarate, analogs of aspartate and glutamate, respectively. Hence, we could cocrystallize ATBSN with succinate or glutarate, and the structures show how the enzyme can bind two kinds of dicarboxylic substrates with different chain lengths. The present results may also provide an insight into the long-standing controversies regarding the mode of binding of glutamate to the wild-type enzyme.


    Related Citations: 
    • Redesigning the Substrate Specificity of an Enzyme by Cumulative Effects of the Mutations of Non-Active Site Residues
      Oue, S., Okamoto, A., Yano, T., Kagamiyama, H.
      (1999) J Biol Chem 274: 2344
    • Directed Evolution of an Aspartate Aminotransferase with New Substrate Specificities
      Yano, T., Oue, S., Kagamiyama, H.
      (1998) Proc Natl Acad Sci U S A 95: 5511

    Organizational Affiliation

    Department of Biochemistry, Osaka Medical College Daigakumachi, Takatsuki, Osaka 569-8686, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ASPARTATE AMINOTRANSFERASE)A396Escherichia coliMutation(s): 15 
EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GUA
Query on GUA

Download Ideal Coordinates CCD File 
C [auth A]GLUTARIC ACID
C5 H8 O4
JFCQEDHGNNZCLN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GUA PDBBind:  1CZC Kd: 1.50e+6 (nM) from 1 assay(s)
Binding MOAD:  1CZC Kd: 1.50e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.35α = 90
b = 85.02β = 90
c = 78.27γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Derived calculations, Refinement description