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12  structures 3  species 0  interactions 126  sequences 14  architectures

Family: VEK-30 (PF12107)

Summary: Plasminogen (Pg) ligand in fibrinolytic pathway

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This is the Wikipedia entry entitled "VEK-30 protein domain". More...

VEK-30 protein domain Edit Wikipedia article

VEK-30
PDB 2doh EBI.jpg
the x-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound a to a peptide from the group a streptococcal surface protein pam
Identifiers
Symbol VEK-30
Pfam PF12107
InterPro IPR021965


In molecular biology, the protein domain VEK-30, is a 30-amino acid long, internal peptide present within bacterial organisms that acts as an epitope or antigenic determinant. It increases the pathogenicity of the cell. More specifically, it is found in streptococcal M-like plasminogen (Pg)-binding protein (PAM) from Gram-positive group-A streptococci (GAS). VEK-30 represents an epitope within PAM that shows high affinity for the lysine binding site (LBS) of the kringle-2 (K2) domain of human (h)Pg.

Plasminogen[edit]

Plasminogen (Pg) is an important mediator of angiostatin production in the fibrinolytic pathway. Plasminogen is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a protein domain of the group A streptococcal protein PAM. It binds to Pg-K2 domain of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C-terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere'.[1]

Function[edit]

Since VEK-30 binds to Pg-K2 domain of angiostatin, its function is crucial to blood clotting, and in lower organisms increase their pathogenicity.

Structure[edit]

In solution, it has been found that VEK-30, exhibited the canonical fold of a kringle domain, including a lack of regular secondary structure. [2]

References[edit]

  1. ^ Cnudde SE, Prorok M, Castellino FJ, Geiger JH (September 2006). "X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM". Biochemistry 45 (37): 11052–60. doi:10.1021/bi060914j. PMID 16964966. 
  2. ^ Wang M, Zajicek J, Geiger JH, Prorok M, Castellino FJ (2010). "Solution structure of the complex of VEK-30 and plasminogen kringle 2.". J Struct Biol 169 (3): 349–59. doi:10.1016/j.jsb.2009.09.011. PMC 2826548. PMID 19800007. 

This article incorporates text from the public domain Pfam and InterPro IPR021965

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Plasminogen (Pg) ligand in fibrinolytic pathway Provide feedback

Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere'. [1]

Literature references

  1. Cnudde SE, Prorok M, Castellino FJ, Geiger JH;, Biochemistry. 2006;45:11052-11060.: X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM. PUBMED:16964966 EPMC:16964966


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021965

Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C-terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere' [PUBMED:16964966].

Domain organisation

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Seed source: pdb_2doh
Previous IDs: none
Type: Domain
Author: Mistry J, Gavin OL
Number in seed: 8
Number in full: 126
Average length of the domain: 16.50 aa
Average identity of full alignment: 71 %
Average coverage of the sequence by the domain: 9.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.9 21.1
Noise cut-off 19.2 20.6
Model length: 17
Family (HMM) version: 3
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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the VEK-30 domain has been found. There are 12 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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