Bacteriocin: Glycocin F
Accession: BAC199
Classification
Class: Unclassified
Genetics
Gene: gccF
Producer and target organisms
Producer Organism: Lactobacillus plantarum [Gram-positive]
Taxonomy: Bacteria
FirmicutesLactobacillalesLactobacillaceaeLactobacillus
Target organismsUnavailable data
Description
STRUCTURE:
Glycocin F, a 43-amino acid bacteriocin from Lactobacillus plantarum, contains two beta-linked N-acetylglucosamine moieties, attached via side chain linkages to a serine (Ser18) via oxygen, and to a cysteine (Cys43) via sulfur.
Glycocin F, a 43-amino acid bacteriocin from Lactobacillus plantarum, contains two beta-linked N-acetylglucosamine moieties, attached via side chain linkages to a serine (Ser18) via oxygen, and to a cysteine (Cys43) via sulfur.
Uniprot and PDB links
UniProt Entry: E9K9Z1
PDB Entry2KUY resolved by NMR.
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 22-64, FUNCTION, SUBCELLULAR LOCATION, MASS SPECTROMETRY, DISULFIDE BONDS, AND GLYCOSYLATION AT SER-39 AND CYS-64, STRAIN=KW30.
PubMed=21251913;DOI=10.1016/j.febslet.2011.01.023
Stepper J., Shastri S., Loo T.S., Preston J.C., Novak P., Man P., Moore C.H., Havlicek V., Patchett M.L., Norris G.E.
"Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins.", FEBS Lett. 585:645-650(2011).
PubMed=21251913;DOI=10.1016/j.febslet.2011.01.023
Stepper J., Shastri S., Loo T.S., Preston J.C., Novak P., Man P., Moore C.H., Havlicek V., Patchett M.L., Norris G.E.
"Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins.", FEBS Lett. 585:645-650(2011).
STRUCTURE BY NMR, DISULFIDE BONDS, AND GLYCOSYLATION AT SER-39 AND CYS-64, STRAIN=KW30.
PubMed=21395300;DOI=10.1021/bi200217u
Venugopal H., Edwards P.J., Schwalbe M., Claridge J.K., Libich D.S., Stepper J., Loo T., Patchett M.L., Norris G.E., Pascal S.M.
"Structural, dynamic, and chemical characterization of a novel s- glycosylated bacteriocin.", Biochemistry 50:2748-2755(2011).
PubMed=21395300;DOI=10.1021/bi200217u
Venugopal H., Edwards P.J., Schwalbe M., Claridge J.K., Libich D.S., Stepper J., Loo T., Patchett M.L., Norris G.E., Pascal S.M.
"Structural, dynamic, and chemical characterization of a novel s- glycosylated bacteriocin.", Biochemistry 50:2748-2755(2011).
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Gene structure
| Gene id | Name | Description | Location |
| BACGene895 | gccI | hypothetical protein putative glycocin F immunity protein | 185..481 |
| BACGene896 | gccH | hypothetical protein | complement(903..1259) |
| BACGene897 | gccA | UDP-GlcNAc glycosyltransferase family 2 | 1310..2578 |
| BACGene898 | gccB | bacteriocin ABC transporter of glycocin F | 2565..4673 |
| BACGene899 | gccC | hypothetical protein | 4670..5089 |
| BACGene900 | gccD | hypothetical protein | 5090..5623 |
| BACGene901 | gccE | putative LytTR response regulator | 5593..6369 |
| BACGene902 | gccF | prebacteriocin glycocin F | 6447..6641 |
Protein sequence
| ........10 ........20 ........30 ........40 ........50 | | | | | KPAWCWYTLA MCGAGYDSGT CDYMYSHCFG IKHHSSGSSS YHC |
Wheel representation
3D Structure
View PDB entry: 2KUY
Protein sequence annotations
| Feature | Position(s) | Length | Description |
| CHAIN | 1↔43 | 43 | Bacteriocin glycocin F. Feature identifier = PRO_5000706231. |
| CARBOHYD | 18 | O-linked (GlcNAc). | |
| CARBOHYD | 43 | S-linked (GlcNAc). | |
| DISULFID | 5↔28 | 24 | |
| DISULFID | 12↔21 | 10 | |
| HELIX | 5↔10 | 6 | |
| STRAND | 16↔19 | 4 | |
| HELIX | 20↔29 | 10 |
Composition
| Amino acid | Count | Percent |
|---|---|---|
| A | 3 | 6.98 % |
| C | 5 | 11.63 % |
| D | 2 | 4.65 % |
| E | 0 | 0.00 % |
| F | 1 | 2.33 % |
| G | 5 | 11.63 % |
| H | 4 | 9.30 % |
| I | 1 | 2.33 % |
| K | 2 | 4.65 % |
| L | 1 | 2.33 % |
| M | 2 | 4.65 % |
| N | 0 | 0.00 % |
| P | 1 | 2.33 % |
| Q | 0 | 0.00 % |
| R | 0 | 0.00 % |
| S | 7 | 16.28 % |
| T | 2 | 4.65 % |
| V | 0 | 0.00 % |
| W | 2 | 4.65 % |
| Y | 5 | 11.63 % |
Hydrophobicity
Composition
| Formula | C0
H0
N0
O0
S0 |
| Absent amino acids | ENQRV |
| Common amino acids | S |
| Mass (Da) | 4 |
| Net charge | +4 |
| Isoelectric point | 7.41 |
| Basic residues | 6 |
| Acidic residues | 2 |
| Hydrophobic residues | 8 |
| Polar residues | 24 |
| Aliphatic residues | 2 |
| Tiny residues | 15 |
| Boman Index | -38.11 |
| Hydropathy Index | -0.319 |
| Aliphatic Index | 25.12 |
| Instability Index | 52.65 (unstable) |
| Half Life |
Mammalian : 1.3 hour Yeast : 3 min E. coli : 2 min |
| Extinction Coefficient | 18700 M-1 cm-1 |
| Absorbance 280nm | 445.24 |