› 5c1e

X-ray diffraction
1.75Å resolution

Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)

Released:
DOI: 10.2210/pdb5c1e/pdb
Model geometry
Fit model/data
PDB entry 5c1e coloured by chain, front view.
PDB entry 5c1e coloured by chain, side view.
PDB entry 5c1e coloured by chain, top view.
Source organism: Aspergillus niger ATCC 1015
Primary publication:
Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control.
Kent LM, Loo TS, Melton LD, Mercadante D, Williams MA, Jameson GB
J Biol Chem 291 1289-306 (2016)
PMID: 26567911

Function and Biology Details

Reaction catalysed: 
Pectin + n H(2)O = n methanol + pectate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124421 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pectinesterase Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 31.79 KDa
Source organism: Aspergillus niger ATCC 1015
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: G3YAL0 (Residues: 29-327; Coverage: 98%)
Gene name: ASPNIDRAFT_214857
Sequence domains: Pectinesterase
Structure domains: Single-stranded right-handed beta-helix, Pectin lyase-like

Ligands and Environments

5 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 5 x SO4
Ligand CL 1 x CL
Ligand GOL 5 x GOL
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007
Spacegroup: C2221
Unit cell:
a: 74.614Å b: 113.543Å c: 88.765Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.202
Expression system: Saccharomyces cerevisiae

Quick links

Citations

10 citation in other articles

Arabidopsis root responses to salinity depend on pectin modification and cell wall sensing.
Gigli-Bisceglia et al. (2022)
9 more

3 mentions without citation

Characterization of an Aspergillus niger for Efficient Fatty Acid Ethyl Ester Synthesis in Aqueous Phase and the Molecular Mechanism.
Xu et al. (2021)
2 more