AMPDB_755 | Midkine-A

1 General Description

AMPDB ID: AMPDB_755

Protein Names: Midkine-A (MK-A) (XMK) (Pleiotrophic factor-alpha-1) (PTF-alpha-1) (X-PTF-alpha1)

Protein Family: Pleiotrophin family

Gene Name: mdk-a

Source Organism: Xenopus laevis (African clawed frog)

Protein Length: 142 AA

Protein Existence: Evidence at transcript level

2 Protein Sequence & Composition

MELRAFCVILLITVLAVSSQAAKNKKEKGKKGASDCTEWTWGSCIPNSKDCGAGTREGTCKEETRKLKCKIPCNWKKAFGADCKYKFENWGECNATTGQKVRSGTLKKALYNADCQQTVEATKPCSLKTKSKSKGKKGKGKE

FASTA format

Counts of Amino Acids

'A': 12, 'R': 4, 'N': 6, 'D': 4, 'C': 11, 'Q': 4, 'E': 10, 'G': 13, 'H': 0, 'I': 4, 'L': 8, 'K': 27, 'M': 1, 'F': 3, 'P': 3, 'S': 9, 'T': 12, 'W': 4, 'Y': 2, 'V': 5

Frequencies of Amino Acids

'A': 8.45%, 'R': 2.82%, 'N': 4.23%, 'D': 2.82%, 'C': 7.75%, 'Q': 2.82%, 'E': 7.04%, 'G': 9.15%, 'H': 0%, 'I': 2.82%, 'L': 5.63%, 'K': 19.01%, 'M': 0.7%, 'F': 2.11%, 'P': 2.11%, 'S': 6.34%, 'T': 8.45%, 'W': 2.82%, 'Y': 1.41%, 'V': 3.52%

Missing Amino Acid(s)

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	15567.1 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	51.62	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	8.774	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.777	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.519	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	10.08	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	16.326	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.183, 0.218, 0.218 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.063	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	24980, 25605	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

Gram Negative Bacteria and Gram Positive Bacteria

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Anti-gram-negative, Anti-gram-Positive

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Signal peptide, Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Fu C, Maminta-Smith LD, Guo C, et al. Cloning and sequence of the Xenopus laevis homologue of the midkine cDNA. Gene. 1994;146(2):311-2. Published 1994 Sep 2. doi:10.1016/0378-1119(94)90312-3

PMID: 8076838

Citation 2: Tsujimura A, Yasojima K, Kuboki Y, et al. Developmental and differential regulations in gene expression of Xenopus pleiotrophic factors-alpha and -beta. Biochem Biophys Res Commun. 1995;214(2):432-9. Published 1995 Sep 14. doi:10.1006/bbrc.1995.2305

PMID: 7677748

Citation 3: Sekiguchi K, Yokota C, Asashima M, et al. Restricted expression of Xenopus midkine gene during early development. J Biochem. 1995;118(1):94-100. Published 1995 Jul. doi:10.1093/oxfordjournals.jbchem.a124898

PMID: 8537332

Citation 4: Zhou H, Muramatsu T, Halfter W, et al. A role of midkine in the development of the neuromuscular junction. Mol Cell Neurosci. 1997;10(1-2):56-70. Published 1997. doi:10.1006/mcne.1997.0638

PMID: 9361288

Citation 5: Yokota C, Takahashi S, Eisaki A, et al. Midkine counteracts the activin signal in mesoderm induction and promotes neural formation. J Biochem. 1998;123(2):339-46. Published 1998 Feb. doi:10.1093/oxfordjournals.jbchem.a021942

PMID: 9538212

Citation 6: Svensson SL, Pasupuleti M, Walse B, et al. Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution. J Biol Chem. 2010;285(21):16105-15. Published 2010 May 21. doi:10.1074/jbc.M109.081232

PMID: 20308059

5.2 Protein Sequence Databases

5.3 3D Structure Databases

AlphaFoldDB: P48530

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	U06048	GenBank \|\| EMBL
2.	D42058	GenBank \|\| EMBL
3.	S80453	GenBank \|\| EMBL
4.	BC108811	GenBank \|\| EMBL

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

PANTHER: PTHR13850

PROSITE: PS00619, PS00620

5.8 Genome Annotation Databases

Ensembl: Not found

KEGG: xla:397791

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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