SUPERFAMILY 1.75 HMM library and genome assignments server

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Midkine superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Midkine [ 57287]
Superfamily:   Midkine [ 57288] (2)
Families:   Midkine, a heparin-binding growth factor, N-terminal domain [ 57289]
  Midkine, a heparin-binding growth factor, C-terminal domain [ 57292]

Superfamily statistics
Genomes (78) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 352 942 2
Proteins 191 517 2

Functional annotation
General category Regulation
Detailed category Other regulatory function

Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR000762 SSF57288 Protein matches
Abstract Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin [PubMed15121180] (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) [PubMed15047154]; retinoic acid-induced heparin-binding protein (RIHB) [PubMed7796887]; and pleiotrophic factors alpha-1and -2 and beta-1 and -2 from Xenopus laevis, the homologs of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a Midkine domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the Midkine superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]