5XQ3 image
Entry Detail
PDB ID:
5XQ3
Keywords:
LYASE
Title:
Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum
Biological Source:
Source Organism:
Penicillium chrysogenum
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2017-06-06
Release Date:
2018-03-21
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.85 Å
R-Value Free:
0.23
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 42 21 2
5XQ3 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:Pcrglx protein
Chain IDs:A
Chain Length:908
Number of Molecules:1
Biological Source:Penicillium chrysogenum
UniProt ID:B6H7Q7 Pfam ID:PF19501, PF21345, PF21346
Protein Blast
Polymer Type:polypeptide(L)
Description:Pcrglx protein
Chain IDs:B
Chain Length:906
Number of Molecules:1
Biological Source:Penicillium chrysogenum
UniProt ID:B6H7Q7 Pfam ID:PF19501, PF21345, PF21346
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET modified residue
Ligand Molecules
CA
Primary Citation
Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
FEBS Lett. 592 1378 1388 (2018)
PMID: 29574769 DOI: 10.1002/1873-3468.13034

Abstact

Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) was recently classified as a member of polysaccharide lyase (PL) family 26 along with hypothetical proteins derived from various organisms. In this study, we determined the crystal structure of PcRGLX as the first structure of a member of this family. Based on the substrate-binding orientation and substrate specificity, PcRGLX is an exo-type PL that cleaves rhamnogalacturonan from the reducing end. Analysis of PcRGLX-complex structures with reaction products indicate that the active site possesses an L-shaped cleft that can accommodate galactosyl side chains, suggesting side-chain-bypassing activity in PcRGLX. Furthermore, we determined the residues critical for catalysis by analyzing the enzyme activities of inactive variants.

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Disease

Primary Citation of related structures
5XQ3