Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

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This is version 1.3 of the entry. See complete history


Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.

Nogues, I.Tramonti, A.Angelaccio, S.Ruszkowski, M.Sekula, B.Contestabile, R.

(2020) Int J Biol Macromol 159: 517-529

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.05.081
  • Primary Citation of Related Structures:  
    6YMD, 6YME, 6YMF

  • PubMed Abstract: 

    Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular one‑carbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions. Although the kinetic properties of AhSHMT correlate with those of the mesophilic orthologue from Escherichia coli, AhSHMT appears more catalytically efficient, especially in presence of salt. Our studies also reveal substrate inhibition, previously unobserved in AhSHMT. Furthermore, addition of the osmoprotectant glycine betaine under salt conditions has a distinct positive effect on AhSHMT activity. The crystal structures of AhSHMT in three forms, as internal aldimine, as external aldimine with the l-serine substrate, and as a covalent complex with malonate, give structural insights on the possible role of specific amino acid residues implicated in the halophilic features of AhSHMT. Importantly, we observed that overexpression of the gene encoding SHMT, independently from its origin, increases the capability of E. coli to grow in high salt conditions, suggesting that the catalytic activity of this enzyme in itself plays a fundamental role in salt tolerance.

  • Organizational Affiliation

    Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Monterotondo, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase
A, B
447Aphanothece halophyticaMutation(s): 0 
Gene Names: glyrAglyA
Find proteins for I7H6W6 (Aphanothece halophytica)
Explore I7H6W6 
Go to UniProtKB:  I7H6W6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7H6W6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C8 H13 N2 O5 P
MLI (Subject of Investigation/LOI)
Query on MLI

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
C3 H2 O4
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B],
L [auth B]
C2 H6 O2
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.05α = 90
b = 94.202β = 90
c = 142.972γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Data collection
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description