Immunoglobulin like domain pfam13895

Associate Editor(s)-in-Chief: Henry A. Hoff

The United States National Library of Medicine (NLM) is a biomedical library in the United States as part of the National Institutes of Health that contains "hierarchical classifications of widely distributed protein domain families [and records] conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research."^[1]

"At the time of writing, the CDD version v3.17 is the live production version with 52,910 protein- and protein domain-models obtained from Pfam (1), SMART (2), the COGs collection (3), TIGRFAMS (4), the NCBI Protein Clusters collection (5), NCBIfam (6) and CDD’s in-house data curation effort (7)."^[1]

Immunoglobulin supergene family

The immunoglobulin supergene family is "the group of proteins that have immunoglobulin-like domains, including histocompatibility antigens, the T-cell antigen receptor, poly-IgR, and other proteins involved in the vertebrate immune response (17)."^[2]

Alpha-1-B glycoprotein variants

Gene ID: 1 A1BG alpha-1-B glycoprotein on 19q13.43: "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins."^[3]

"𝛂₁B-glycoprotein(𝛂₁B) [...] consists of a single polypeptide chain N-linked to four glucosamine oligosaccharides. The polypeptide has five intrachain disulfide bonds and contains 474 amino acid residues. [...] 𝛂₁B exhibits internal duplication and consists of five repeating structural domains, each containing about 95 amino acids and one disulfide bond. [...] several domains of 𝛂₁B, especially the third, show statistically significant homology to variable regions of certain immunoglobulin light and heavy chains. 𝛂₁B [...] exhibits sequence similarity to other members of the immunoglobulin supergene family such as the receptor for transepithelial transport of IgA and IgM and the secretory component of human IgA."^[2]

"Some of the domains of 𝛂₁B show significant homology to variable (V) and constant (C) regions of certain immunoglobulins. Likewise, there is statistically significant homology between 𝛂₁B and the secretory component (SC) of human IgA (15) and also with the extracellular portion of the rabbit receptor for transepithelial transport of polymeric immunoglobulins (IgA and IgM). Mostov et al. (16) have called the later protein the poly-Ig receptor or poly-IgR and have shown that it is the precursor of SC."^[2]

"𝛂₁B-glycoprotein(𝛂₁B) [...] consists of a single polypeptide chain N-linked to four glucosamine oligosaccharides. The polypeptide has five intrachain disulfide bonds and contains 474 amino acid residues. [...] 𝛂₁B exhibits internal duplication and consists of five repeating structural domains, each containing about 95 amino acids and one disulfide bond. [...] several domains of 𝛂₁B, especially the third, show statistically significant homology to variable regions of certain immunoglobulin light and heavy chains. 𝛂₁B [...] exhibits sequence similarity to other members of the immunoglobulin supergene family such as the receptor for transepithelial transport of IgA and IgM and the secretory component of human IgA."^[2]

A1BG contains the immunoglobulin domain: cl11960 and three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

"This domain [pfam13895] contains immunoglobulin-like domains."^[4]

Carcinoembryonic antigen gene family

Immunoglobulin superfamily genes

Major histocompatibility complex genes

Class I

Class II

Class III

Immunoglobulin domain genes

Immunoglobulin receptor superfamily

Genes having immunoglobulin like domain pfam13895

Gene ID: 1 see Immunoglobulin domain genes.

Gene ID: 177 see Major histocompatibility complex class III gene family.

Gene ID: 634 see Carcinoembryonic antigen gene family.

Gene ID: 942 is CD86

Gene ID: 962 is CD48

Gene ID: 1048 see Carcinoembryonic antigen gene family.

Gene ID: 1088 is CEACAM8.

Gene ID: 2324 is FLT4

Gene ID: 3339 is HSPG2

Gene ID: 3385 see Carcinoembryonic antigen gene family.

Gene ID: 3791 see Immunoglobulin like domain smart00410.

Gene ID: 3902 is LAG3

Gene ID: 4059 see Carcinoembryonic antigen gene family.

Gene ID: 4680 see Carcinoembryonic antigen gene family.

Gene ID: 4756 is NEO1

Gene ID: 5175 see Carcinoembryonic antigen gene family.

Gene ID: 5669 is PSG1

Gene ID: 5670 is PSG2

Gene ID: 5671 is PSG3

Gene ID: 5672 is PSG4

Gene ID: 5673 is PSG5

Gene ID: 5675 is PSG6

Gene ID: 5676 is PSG7

Gene ID: 5678 is PSG9

Gene ID: 5680 is PSG11

Gene ID: 6614 is SIGLEC1

Gene ID: 7087 see Carcinoembryonic antigen gene family.

Gene ID: 7273 see Immunoglobulin like domain smart00410.

Gene ID: 10892 is MALT1

Gene ID: 27036 is SIGLEC7

Gene ID: 51744 is CD244

Gene ID: 55243 is KIRREL1

Gene ID: 57611 is ISLR2

Gene ID: 57863 see Carcinoembryonic antigen gene family.

Gene ID: 79368 see Immunoglobulin receptor superfamily genes.

Gene ID: 79827 is CLMP

Gene ID: 83416 see Immunoglobulin receptor superfamily genes.

Gene ID: 83417 see Immunoglobulin receptor superfamily genes.

Gene ID: 84033 is OBSCN

Gene ID: 84623 is KIRREL3

Gene ID: 84824 is FCRLA

Gene ID: 115350 see Immunoglobulin receptor superfamily genes.

Gene ID: 115352 see Immunoglobulin receptor superfamily genes.

Gene ID: 125931 see Carcinoembryonic antigen gene family.

Gene ID: 161357 is MDGA2

Gene ID: 220296 see Carcinoembryonic antigen gene family.

Gene ID: 255809 is C19orf38

Gene ID: 284021 is MILR1

Gene ID: 343413 see Immunoglobulin receptor superfamily genes.

Gene ID: 388551 see Carcinoembryonic antigen gene family.

Gene ID: 440533 is PSG8

Hypotheses

Downstream core promoters may work as transcription factors even as their complements or inverses.
In addition to the DNA binding sequences listed above, the transcription factors that can open up and attach through the local epigenome need to be known and specified.
The function of A1BG is the same as other immunoglobulin genes possessing the immunoglobulin domain cl11960 and/or any of three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

References

↑ ^1.0 ^1.1 Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J Lanczycki, and Aron Marchler-Bauer (8 January 2020). "CDD/SPARCLE: The Conserved Domain Database in 2020". Nucleic Acids Research. 48 (D1): D265–D268. doi:10.1093/nar/gkz991. PMID 31777944. Retrieved 24 June 2020.
↑ ^2.0 ^2.1 ^2.2 ^2.3 Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (April 1986). "Amino acid sequence of human plasma 𝛂₁B-glycoprotein: Homology to the immunoglobulin supergene family" (PDF). Proceedings of the National Academy of Sciences USA. 83 (8): 2363–7. doi:10.1073/pnas.83.8.2363. PMID 3458201. Retrieved 9 March 2020.
↑ RefSeq (July 2008). "A1BG alpha-1-B glycoprotein [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 17 April 2020.
↑ NCBI (5 August 2015). "Conserved Protein Domain Family pfam13895: Ig_2". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 May 2020.

External links

{{Phosphate biochemistry}}Template:Sisterlinks

[Lu-1] 1.0 ^1.1 Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J Lanczycki, and Aron Marchler-Bauer (8 January 2020). "CDD/SPARCLE: The Conserved Domain Database in 2020". Nucleic Acids Research. 48 (D1): D265–D268. doi:10.1093/nar/gkz991. PMID 31777944. Retrieved 24 June 2020.

[Ishioka-2] 2.0 ^2.1 ^2.2 ^2.3 Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (April 1986). "Amino acid sequence of human plasma 𝛂₁B-glycoprotein: Homology to the immunoglobulin supergene family" (PDF). Proceedings of the National Academy of Sciences USA. 83 (8): 2363–7. doi:10.1073/pnas.83.8.2363. PMID 3458201. Retrieved 9 March 2020.

[RefSeq1-3] RefSeq (July 2008). "A1BG alpha-1-B glycoprotein [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 17 April 2020.

[NCBI372793-4] NCBI (5 August 2015). "Conserved Protein Domain Family pfam13895: Ig_2". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 May 2020.

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