Summary: Formate dehydrogenase N, transmembrane

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Wikipedia: Formate dehydrogenase
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Formate dehydrogenase Edit Wikipedia article

Formate dehydrogenase N, transmembrane

Identifiers

Symbol

Form-deh_trans

1kqf / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary
PDB	1kqfB:246-289 1kqgB:246-289

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]

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⁺ â‡Œ CO₂ + NADH + H⁺

Cytochrome-dependent reaction

Formate + 2 ferricytochrome b1 â‡Œ 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]

References

^ Ferry JG (1990). "Formate dehydrogenase". FEMS Microbiol. Rev. 7 (3â€“4): 377â€“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): 625â€“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): 418â€“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): 627â€“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): 720â€“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): 3518â€“3528. doi:10.1021/bi972177k. PMID 9521673.
^ Jormakka M, TÃ¶rnroth S, Byrne B, Iwata S (2002). "Molecular basis of proton motive force generation: structure of formate dehydrogenase-N". Science. 295 (5561): 1863â€“1868. doi:10.1126/science.1068186. PMID 11884747.

External links

Metabolism: Citric acid cycle enzymes

Cycle

Anaplerotic

to acetyl-CoA	Pyruvate dehydrogenase complex (E1, E2, E3) (regulated by Pyruvate dehydrogenase kinase and Pyruvate dehydrogenase phosphatase)
to Î±-ketoglutaric acid	Glutamate dehydrogenase
to succinyl-CoA	Methylmalonyl-CoA mutase
to oxaloacetate	Pyruvate carboxylase Aspartate transaminase

Mitochondrial
electron transport chain/
oxidative phosphorylation

Primary	Complex I/NADH dehydrogenase Complex II/Succinate dehydrogenase Coenzyme Q Complex III/Coenzyme Q - cytochrome c reductase Cytochrome c Complex IV/Cytochrome c oxidase Coenzyme Q10 synthesis: COQ2 COQ3 COQ4 COQ5 COQ6 COQ7 COQ9 COQ10A COQ10B PDSS1 PDSS2
Other	Alternative oxidase Electron-transferring-flavoprotein dehydrogenase

Metabolism, catabolism, anabolism

General

Energy
metabolism

Aerobic respiration	Glycolysis â†’ Pyruvate decarboxylation â†’ Citric acid cycle â†’ Oxidative phosphorylation (electron transport chain + ATP synthase)
Anaerobic respiration	Electron acceptors are other than oxygen
Fermentation	Glycolysis â†’ Substrate-level phosphorylation ABE Ethanol Lactic acid

Specific
paths

Protein metabolism

Carbohydrate metabolism
(carbohydrate catabolism
and anabolism)

Human

Glycolysis â‡„ Gluconeogenesis
Glycogenolysis â‡„ Glycogenesis
Pentose phosphate pathway Fructolysis Galactolysis
Glycosylation N-linked O-linked

Nonhuman

Photosynthesis Anoxygenic photosynthesis Chemosynthesis Carbon fixation
Xylose metabolism Radiotrophism

Lipid metabolism
(lipolysis, lipogenesis)

Fatty acid metabolism	Fatty acid degradation (Beta oxidation) Fatty acid synthesis
Other	Steroid metabolism Sphingolipid metabolism Eicosanoid metabolism Ketosis Reverse cholesterol transport

Amino acid

Nucleotide
metabolism

Other

v t e Aldehyde/oxo oxidoreductases (EC 1.2)
1.2.1: NAD or NADP	Aldehyde dehydrogenase Acetaldehyde dehydrogenase Long-chain-aldehyde dehydrogenase
1.2.2: cytochrome	Formate dehydrogenase (cytochrome)
1.2.3: oxygen	Aldehyde oxidase
1.2.4: disulfide	Oxoglutarate dehydrogenase complex Pyruvate dehydrogenase Branched-chain alpha-keto acid dehydrogenase complex BCKDHA BCKDHB DBT DLD
1.2.7: iron-sulfur protein	Pyruvate synthase

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadieâ€“Hofstee diagram Hanesâ€“Woolf plot Lineweaverâ€“Burk plot Michaelisâ€“Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

This EC 1.2 enzyme-related article is a stub. You can help Wikipedia by expanding it.

This article about metabolism is a stub. You can help Wikipedia by expanding it.

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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

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

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (50)	Full (539)	Representative proteomes				UniProt (4838)	NCBI (5942)	Meta (11)
	Seed (50)	Full (539)	RP15 (42)	RP35 (176)	RP55 (514)	RP75 (1349)	UniProt (4838)	NCBI (5942)	Meta (11)
Jalview	View	View	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (50)	Full (539)	Representative proteomes				UniProt (4838)	NCBI (5942)	Meta (11)
	Seed (50)	Full (539)	RP15 (42)	RP35 (176)	RP55 (514)	RP75 (1349)	UniProt (4838)	NCBI (5942)	Meta (11)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (50)	Full (539)	Representative proteomes				UniProt (4838)	NCBI (5942)	Meta (11)
	Seed (50)	Full (539)	RP15 (42)	RP35 (176)	RP55 (514)	RP75 (1349)	UniProt (4838)	NCBI (5942)	Meta (11)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

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

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.1	22.1
Trusted cut-off	22.3	22.5
Noise cut-off	21.1	21.6

Model length:

44

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

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How the sunburst is generated

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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Interactions

There are 3 interactions for this family. More...

Cytochrome_B Fer4_11 Fer4_9

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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Family: Form-deh_trans (PF09163)

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