3GSB

CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE IN COMPLEX WITH GABACULINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of glutamate-1-semialdehyde aminomutase: an alpha2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity.

Hennig, M.Grimm, B.Contestabile, R.John, R.A.Jansonius, J.N.

(1997) Proc Natl Acad Sci U S A 94: 4866-4871

  • DOI: https://doi.org/10.1073/pnas.94.10.4866
  • Primary Citation of Related Structures:  
    2GSA, 3GSB, 4GSA

  • PubMed Abstract: 

    The three-dimensional structure of glutamate-1-semialdehyde aminomutase (EC 5.4.3.8), an alpha2-dimeric enzyme from Synechococcus, has been determined by x-ray crystallography using heavy atom derivative phasing. The structure, refined at 2.4-A resolution to an R-factor of 18.7% and good stereochemistry, explains many of the enzyme's unusual specificity and functional properties. The overall fold is that of aspartate aminotransferase and related B6 enzymes, but it also has specific features. The structure of the complex with gabaculine, a substrate analogue, shows unexpectedly that the substrate binding site involves residues from the N-terminal domain of the molecule, notably Arg-32. Glu-406 is suitably positioned to repel alpha-carboxylic acids, thereby suggesting a basis for the enzyme's reaction specificity. The subunits show asymmetry in cofactor binding and in the mobilities of the residues 153-181. In the unliganded enzyme, one subunit has the cofactor bound as an aldimine of pyridoxal phosphate with Lys-273 and, in this subunit, residues 153-181 are disordered. In the other subunit in which the cofactor is not covalently bound, residues 153-181 are well defined. Consistent with the crystallographically demonstrated asymmetry, a form of the enzyme in which both subunits have pyridoxal phosphate bound to Lys-273 through a Schiff base showed biphasic reduction by borohydride in solution. Analysis of absorption spectra during reduction provided evidence of communication between the subunits. The crystal structure of the reduced form of the enzyme shows that, despite identical cofactor binding in each monomer, the structural asymmetry at residues 153-181 remains.


  • Organizational Affiliation

    Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE)
A, B
432Synechococcus sp.Mutation(s): 0 
EC: 5.4.3.8
UniProt
Find proteins for P24630 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P24630 
Go to UniProtKB:  P24630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24630
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
GAB
Query on GAB

Download Ideal Coordinates CCD File 
D [auth A]3-AMINOBENZOIC ACID
C7 H7 N O2
XFDUHJPVQKIXHO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.6α = 90
b = 108.6β = 90
c = 123.5γ = 90
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-17
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description