5HDM

Crystal structure of Arabidopsis thaliana glutamate-1-semialdehyde-2,1-aminomutase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.128 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana.

Song, Y.Pu, H.Jiang, T.Zhang, L.Ouyang, M.

(2016) Acta Crystallogr F Struct Biol Commun 72: 448-456

  • DOI: 10.1107/S2053230X16007263
  • Primary Citation of Related Structures:  
    5HDM

  • PubMed Abstract: 
  • Glutamate-1-semialdehyde-2,1-aminomutase (GSAM) catalyzes the isomerization of glutamate-1-semialdehyde (GSA) to 5-aminolevulinate (ALA) and is distributed in archaea, most bacteria and plants. Although structures of GSAM from archaea and bacteria ha ...

    Glutamate-1-semialdehyde-2,1-aminomutase (GSAM) catalyzes the isomerization of glutamate-1-semialdehyde (GSA) to 5-aminolevulinate (ALA) and is distributed in archaea, most bacteria and plants. Although structures of GSAM from archaea and bacteria have been resolved, a GSAM structure from a higher plant is not available, preventing further structure-function analysis. Here, the structure of GSAM from Arabidopsis thaliana (AtGSA1) obtained by X-ray crystallography is reported at 1.25 Å resolution. AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation, which is consistent with previously reported Synechococcus GSAM structures. While one monomer binds PMP with the gating loop fixed in the open state, the other monomer binds either PMP or PLP and the gating loop is ready to close. The data also reveal the mobility of residues Gly163, Ser164 and Gly165, which are important for reorientation of the gating loop. Furthermore, the asymmetry of the AtGSA1 structure supports the previously proposed negative cooperativity between monomers of GSAM.


    Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplasticAB434Arabidopsis thalianaMutation(s): 0 
Gene Names: GSA1HEML1At5g63570MBK5.3
EC: 5.4.3.8
Find proteins for P42799 (Arabidopsis thaliana)
Explore P42799 
Go to UniProtKB:  P42799
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP

Download CCD File 
A, B
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.128 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.117α = 90
b = 109.331β = 90
c = 115.502γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
ARPmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-05 
  • Released Date: 2016-06-15 
  • Deposition Author(s): Song, Y., Pu, H., Liu, L.

Funding OrganizationLocationGrant Number
National Natural Science Fundation of ChinaChina31471267

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references, Derived calculations