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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0132

PubMed

30341165, Biochem J. 2018 Nov 28;475(22):3609-3628. doi: 10.1042/BCJ20180486.

Characterization method

enzyme activity assay

Genomic accession number

FP476056.1

Nucelotide position range

249036-267488

Substrate

hemicellulose

Loci

ZOBELLIA_208-ZOBELLIA_215

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

engA ZOBELLIA_208 CAZ94281.1 0 - 1194 (-) FP476056.1:249036-250230 3.2.1.4
- ZOBELLIA_209 CAZ94282.1 1414 - 3004 (-) FP476056.1:250450-252040 -
- ZOBELLIA_210 CAZ94283.1 3013 - 4039 (-) FP476056.1:252049-253075 -
- ZOBELLIA_211 CAZ94284.1 4102 - 5830 (-) FP476056.1:253138-254866 -
- ZOBELLIA_212 CAZ94285.1 5849 - 8699 (-) FP476056.1:254885-257735 -
- ZOBELLIA_213 CAZ94286.1 8736 - 10545 (-) FP476056.1:257772-259581 -
- ZOBELLIA_214 CAZ94287.1 10556 - 13655 (-) FP476056.1:259592-262691 -
- ZOBELLIA_215 CAZ94288.1 14325 - 18453 (-) FP476056.1:263361-267489 2.7.13.3

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

engA 1 - 1194 (-) CAZyme: GH5|GH5_4 Yes
- 1415 - 3004 (-) CAZyme: CBM4 Yes
- 3014 - 4039 (-) other Yes
- 4103 - 5830 (-) other Yes
- 5850 - 8699 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 8737 - 10545 (-) other Yes
- 10557 - 13655 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 14326 - 18453 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0132

PubMed

30341165, Biochem J. 2018 Nov 28;475(22):3609-3628. doi: 10.1042/BCJ20180486.

Title

The laterally acquired GH5 ZgEngA(GH5_4) from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis.

Author

Dorival J, Ruppert S, Gunnoo M, Orlowski A, Chapelais-Baron M, Dabin J, Labourel A, Thompson D, Michel G, Czjzek M, Genicot S

Abstract

Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (beta-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase (ZgEngA(GH5_4)). A phylogenetic analysis indicates that ZgEngA(GH5_4) was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of ZgEngA(GH5_4) and demonstrated that this GH5 is, in fact, an endo-beta-glucanase, most active on mixed-linked glucan (MLG). Although ZgEngA(GH5_4) and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of ZgEngA(GH5_4) reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose-binding subsites are conserved, when compared with the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose-binding subsites of ZgEngA(GH5_4) are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared with the structures of other GH5_4 enzymes.