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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0155

PubMed

16545947, Res Microbiol. 2006 Sep;157(7):642-9. doi: 10.1016/j.resmic.2006.02.006. Epub 2006 Mar 2.

Characterization method

enzyme activity assay

Genomic accession number

AE007870.2

Nucelotide position range

11703-21103

Substrate

alginate

Loci

atu3019-atu3026

Species

Agrobacterium fabrum/1176649

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Atu3019 AAK90364.2 0 - 537 (-) AE007870.2:11703-12240 -
- Atu3020 AAK90363.2 968 - 1679 (+) AE007870.2:12671-13382 -
- Atu3021 AAK90362.1 1709 - 2825 (+) AE007870.2:13412-14528 -
- Atu3022 AAK90361.1 2821 - 3751 (+) AE007870.2:14524-15454 -
- Atu3023 AAK90360.1 3762 - 4644 (+) AE007870.2:15465-16347 -
- Atu3024 AAK90359.2 4704 - 6234 (+) AE007870.2:16407-17937 -
- Atu3025 AAK90358.1 6305 - 8636 (+) AE007870.2:18008-20339 -
- Atu3026 AAK90357.1 8651 - 9401 (+) AE007870.2:20354-21104 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 537 (-) CDS No
- 969 - 1679 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No
- 1710 - 2825 (+) TC: gnl|TC-DB|Q9KWT9|3.A.1.1.10 Yes
- 2822 - 3751 (+) TC: gnl|TC-DB|Q9KWT8|3.A.1.1.10 Yes
- 3763 - 4644 (+) TC: gnl|TC-DB|Q9KWT7|3.A.1.1.10 Yes
- 4705 - 6234 (+) TC: gnl|TC-DB|Q9KWT6|3.A.1.1.10 Yes
- 6306 - 8636 (+) CAZyme: PL15_1 Yes
- 8652 - 9401 (+) CDS No

PUL ID

PUL0155

PubMed

16545947, Res Microbiol. 2006 Sep;157(7):642-9. doi: 10.1016/j.resmic.2006.02.006. Epub 2006 Mar 2.

Title

A biosystem for alginate metabolism in Agrobacterium tumefaciens strain C58: molecular identification of Atu3025 as an exotype family PL-15 alginate lyase.

Author

Ochiai A, Hashimoto W, Murata K

Abstract

The Gram-negative bacterium Sphingomonas sp. strain A1 (strain A1) has a peculiar biosystem to directly import and depolymerize a macromolecule, alginate, which is encoded by a cluster of genes on the genome. We identified five clustered ORFs homologous to some genes of the strain A1 cluster in the genome of Agrobacterium tumefaciens strain C58 (strain C58). These ORFs are Atu3021, Atu3022, Atu3023, and Atu3024, encoding a putative sugar ABC transporter system and Atu3025, which encodes a putative alginate lyase. We analyzed the involvement of this gene cluster in alginate metabolism. Strain C58 cells grew significantly on low-molecular-weight (LMW) alginate (average molecular weight, 1000), and we detected specific alginate-induced expression of Atu3024 and Atu3025. This strain does not grow on alginate (average molecular weight, 25,600), suggesting that the strain C58 gene cluster is involved in importing and degrading LMW alginate. One protein, Atu3025, purified from strain C58, was identified as an alginate lyase, and the enzyme overexpressed in Escherichia coli was further characterized. Atu3025 released monosaccharides specifically from alginate most efficiently at pH 7.3 and 30 degrees C through a beta-elimination reaction, indicating that Atu3025 is an exotype alginate lyase potentially involved in the assimilation of LMW alginate in strain C58.