Summary: Formate dehydrogenase N, transmembrane
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Formate dehydrogenase Edit Wikipedia article
Formate dehydrogenase N, transmembrane | |||||||||||
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Identifiers | |||||||||||
Symbol | Form-deh_trans | ||||||||||
Pfam | PF09163 | ||||||||||
InterPro | IPR015246 | ||||||||||
SCOPe | 1kqf / SUPFAM | ||||||||||
OPM superfamily | 3 | ||||||||||
OPM protein | 1kqf | ||||||||||
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Formate dehydrogenases are a set of enzymes that catalyse the oxidation of formate to carbon dioxide, donating the electrons to a second substrate, such as NAD+ in formate:NAD+ oxidoreductase (EC 1.2.1.2) or to a cytochrome in formate:ferricytochrome-b1 oxidoreductase (EC 1.2.2.1).[1]
Contents
Function
NAD-dependent formate dehydrogenases are important in methylotrophic yeast and bacteria and are vital in the catabolism of C1 compounds such as methanol.[2] The cytochrome-dependent enzymes are more important in anaerobic metabolism in prokaryotes.[3] For example, in E. coli, the formate:ferricytochrome-b1 oxidoreductase is an intrinsic membrane protein with two subunits and is involved in anaerobic nitrate respiration.[4][5]
NAD-dependent reaction
Formate + NAD+ ⇌ CO2 + NADH + H+
Cytochrome-dependent reaction
Formate + 2 ferricytochrome b1 ⇌ CO2 + 2 ferrocytochrome b1 + 2 H+
Molybdopterin, molybdenum and selenium dependence
One of the enzymes in the oxidoreductase family that sometimes employ tungsten (bacterial formate dehydrogenase H) is known to use a selenium-molybdenum version of molybdopterin.[6]
Transmembrane domain
The transmembrane domain of the beta subunit of formate dehydrogenase consists of a single transmembrane helix. This domain acts as a transmembrane anchor, allowing the conduction of electrons within the protein.[7]
See also
- Formate dehydrogenase (cytochrome)
- Formate dehydrogenase (cytochrome-c-553)
- Formate dehydrogenase (NADP+)
- Microbial metabolism
References
- ^ Ferry JG (1990). "Formate dehydrogenase". FEMS Microbiol. Rev. 7 (3–4): 377–82. doi:10.1111/j.1574-6968.1990.tb04940.x. PMID 2094290.
- ^ Popov VO, Lamzin VS (1994). "NAD(+)-dependent formate dehydrogenase". Biochem. J. 301 (3): 625–43. PMC 1137035. PMID 8053888.
- ^ Jormakka M, Byrne B, Iwata S (2003). "Formate dehydrogenase--a versatile enzyme in changing environments". Curr. Opin. Struct. Biol. 13 (4): 418–23. doi:10.1016/S0959-440X(03)00098-8. PMID 12948771.
- ^ Graham A, Boxer DH (1981). "The organization of formate dehydrogenase in the cytoplasmic membrane of Escherichia coli". Biochem. J. 195 (3): 627–37. PMC 1162934. PMID 7032506.
- ^ Ruiz-Herrera J, DeMoss JA (1969). "Nitrate reductase complex of Escherichia coli K-12: participation of specific formate dehydrogenase and cytochrome b1 components in nitrate reduction". J. Bacteriol. 99 (3): 720–9. PMC 250087. PMID 4905536.
- ^ Khangulov SV, Gladyshev VN, Dismukes GC, Stadtman TC (1998). "Selenium-Containing Formate Dehydrogenase H from Escherichia coli: A Molybdopterin Enzyme That Catalyzes Formate Oxidation without Oxygen Transfer". Biochemistry. 37 (10): 3518–3528. doi:10.1021/bi972177k. PMID 9521673.
- ^ Jormakka M, Törnroth S, Byrne B, Iwata S (2002). "Molecular basis of proton motive force generation: structure of formate dehydrogenase-N". Science. 295 (5561): 1863–1868. doi:10.1126/science.1068186. PMID 11884747.
External links
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Formate dehydrogenase N, transmembrane Provide feedback
Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein [1].
Literature references
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Jormakka M, Tornroth S, Byrne B, Iwata S; , Science. 2002;295:1863-1868.: Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. PUBMED:11884747 EPMC:11884747
External database links
SCOP: | 1kqf |
This tab holds annotation information from the InterPro database.
InterPro entry IPR015246
The transmembrane domain of the beta subunit of formate dehydrogenase consists of a single transmembrane helix. This domain acts as a transmembrane anchor, allowing the conduction of electrons within the protein [PUBMED:11884747].
Domain organisation
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Alignments
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Seed (50) |
Full (539) |
Representative proteomes | UniProt (4838) |
NCBI (5942) |
Meta (11) |
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RP15 (42) |
RP35 (176) |
RP55 (514) |
RP75 (1349) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (50) |
Full (539) |
Representative proteomes | UniProt (4838) |
NCBI (5942) |
Meta (11) |
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RP15 (42) |
RP35 (176) |
RP55 (514) |
RP75 (1349) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
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Curation
Seed source: | pdb_1kqf |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Sammut SJ |
Number in seed: | 50 |
Number in full: | 539 |
Average length of the domain: | 43.70 aa |
Average identity of full alignment: | 44 % |
Average coverage of the sequence by the domain: | 14.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 44 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
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Interactions
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 Form-deh_trans domain has been found. There are 2 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 sequence.
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