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2  structures 834  species 1  interaction 1298  sequences 17  architectures

Family: Form-deh_trans (PF09163)

Summary: Formate dehydrogenase N, transmembrane

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This is the Wikipedia entry entitled "Formate dehydrogenase". More...

Formate dehydrogenase Edit Wikipedia article

Formate dehydrogenase N, transmembrane
Identifiers
Symbol Form-deh_trans
Pfam PF09163
InterPro IPR015246
SCOP 1kqf
SUPERFAMILY 1kqf
OPM superfamily 3
OPM protein 1kqf

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]

Biological function[edit]

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[edit]

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[edit]

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[edit]

References[edit]

  1. ^ Ferry JG (1990). "Formate dehydrogenase". FEMS Microbiol. Rev. 7 (3–4): 377–82. PMID 2094290. 
  2. ^ Popov VO, Lamzin VS (1994). "NAD(+)-dependent formate dehydrogenase". Biochem. J. 301 (3): 625–43. PMC 1137035. PMID 8053888. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ Khangulov, S. V. et al. (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. 
  7. ^ Iwata S, Byrne B, Tornroth S, Jormakka M (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[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

  1. 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

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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RP75
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  Seed
(40)
Full
(1298)
Representative proteomes NCBI
(480)
Meta
(11)
RP15
(20)
RP35
(52)
RP55
(94)
RP75
(134)
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  Seed
(40)
Full
(1298)
Representative proteomes NCBI
(480)
Meta
(11)
RP15
(20)
RP35
(52)
RP55
(94)
RP75
(134)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Seed source: pdb_1kqf
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 40
Number in full: 1298
Average length of the domain: 44.10 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 14.80 %

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 20.6 20.6
Trusted cut-off 20.9 20.9
Noise cut-off 20.2 20.5
Model length: 44
Family (HMM) version: 6
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Species distribution

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Interactions

There is 1 interaction for this family. More...

Fer4

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 seqence.

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