5XQO

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate

Summary for 5XQO

• Entry DOI: 10.2210/pdb5xqo/pdb
• Descriptor: Pcrglx protein, 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose, 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose, ... (5 entities in total)
• Functional Keywords: exo-rhamnogalacturonan lyase, enzyme, pectin, sad, se, lyase
• Biological source: Penicillium chrysogenum
• Total number of polymer chains: 2
• Total formula weight: 202950.18

Authors

Kunishige, Y.,Iwai, M.,Tada, T.,Nishimura, S.,Sakamoto, T. (deposition date: 2017-06-07, release date: 2018-03-21, Last modification date: 2023-11-22)

Primary citation

Kunishige, Y.,Iwai, M.,Nakazawa, M.,Ueda, M.,Tada, T.,Nishimura, S.,Sakamoto, T.
Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
FEBS Lett., 592:1378-1388, 2018

PubMed Abstract: 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.

PubMed: 29574769
DOI: 10.1002/1873-3468.13034

Experimental method

X-RAY DIFFRACTION (3.2 Å)