AMPDB_26 | Antifungal protein ginkbilobin-2

1 General Description

AMPDB ID: AMPDB_26

Protein Names: Antifungal protein ginkbilobin-2 (Antimicrobial protein Gnk2-1)

Protein Family: Nil

Gene Name: GNK2 GNK2-1

Source Organism: Ginkgo biloba (Ginkgo) (Maidenhair tree)

Protein Length: 134 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MKTMRMNSAFILAFALAAAMLILTEAANTAFVSSACNTQKIPSGSPFNRNLRAMLADLRQNTAFSGYDYKTSRAGSGGAPTAYGRATCKQSISQSDCTACLSNLVNRIFSICNNAIGARVQLVDCFIQYEQRSF

FASTA format

Counts of Amino Acids

'A': 20, 'R': 9, 'N': 10, 'D': 4, 'C': 6, 'Q': 7, 'E': 2, 'G': 7, 'H': 0, 'I': 8, 'L': 10, 'K': 4, 'M': 5, 'F': 8, 'P': 3, 'S': 14, 'T': 9, 'W': 0, 'Y': 4, 'V': 4

Frequencies of Amino Acids

'A': 14.93%, 'R': 6.72%, 'N': 7.46%, 'D': 2.99%, 'C': 4.48%, 'Q': 5.22%, 'E': 1.49%, 'G': 5.22%, 'H': 0%, 'I': 5.97%, 'L': 7.46%, 'K': 2.99%, 'M': 3.73%, 'F': 5.97%, 'P': 2.24%, 'S': 10.45%, 'T': 6.72%, 'W': 0%, 'Y': 2.99%, 'V': 2.99%

Missing Amino Acid(s)

H, W

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

Hydrophobic Amino Acid(s) Count

Hydrophilic Amino Acid(s) Count

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

Modified Amino Acid(s) Count

Modified Amino Acid(s) Frequencies

Computed by biopython (version 1.79) & proteinAnalysis (version 1)

3 Physicochemical Properties

Sl. No.	Properties	Values	Reference
1.	Molecular Mass	14472.6 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	75.97	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	48.242	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	0.051	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.639	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	9.395	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	6.627	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.254, 0.254, 0.276 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.09	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	5960, 6335	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

F.culmorum, F.oxysporum, S.cerevisiae, T.reesei

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Fungicide, Plant defense, Anti-candida, Anti-yeast

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Lectin, Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Sawano Y, Miyakawa T, Yamazaki H, et al. Purification, characterization, and molecular gene cloning of an antifungal protein from Ginkgo biloba seeds. Biol Chem. 2007;388(3):273-80. Published 2007 Mar. doi:10.1515/BC.2007.030

PMID: 17338634

Citation 2: Gao N, Wadhwani P, MÃ¼hlhÃ¤user P, et al. An antifungal protein from Ginkgo biloba binds actin and can trigger cell death. Protoplasma. 2016;253(4):1159-74. Published 2016 Jul. doi:10.1007/s00709-015-0876-4

PMID: 26315821

Citation 3: Miyakawa T, Sawano Y, Miyazono K, et al. Crystallization and preliminary X-ray analysis of ginkbilobin-2 from Ginkgo biloba seeds: a novel antifungal protein with homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63(Pt 9):737-9. Published 2007 Sep 1. doi:10.1107/S1744309107034793

PMID: 17768341

Citation 4: Miyakawa T, Miyazono K, Sawano Y, et al. Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Proteins. 2009;77(1):247-51. Published 2009 Oct. doi:10.1002/prot.22494

PMID: 19603485

Citation 5: Miyakawa T, Hatano K, Miyauchi Y, et al. A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity. Plant Physiol. 2014;166(2):766-78. Published 2014 Oct. doi:10.1104/pp.114.242636

PMID: 25139159

Citation 6: , . Corrections. Plant Physiol. 2015;167(3):1204. Published 2015 Mar. doi:10.1104/pp.115.900504

PMID: 25725072

5.2 Protein Sequence Databases

5.3 3D Structure Databases

	Sl. no.	PDB ID	Method	Resolution	Access Links	3D View

AlphaFoldDB: A4ZDL6

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	DQ496113	GenBank \|\| EMBL
2.	FJ822053	GenBank \|\| EMBL
3.	FJ865399	GenBank \|\| EMBL

RefSeq: Not found

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: Not found

BioGRID: Not found

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

InterPro: IPR002902, IPR038408

PANTHER: Not found

PROSITE: PS51473

5.8 Genome Annotation Databases

Ensembl: Not found

5.9 Phylogenomic Databases

GeneTree: Not found

5.10 Enzyme & Pathway Databases

BRENDA: Not found

BioCyc: Not found

5.11 Protein-RNA Interaction Databases

RNAct: Not found

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