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

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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]

References[edit]

^ Ferry JG (1990). "Formate dehydrogenase". FEMS Microbiol. Rev. 7 (3–4): 377–82. 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, 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.
^ 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]

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 α-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

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

Metabolism (Catabolism, Anabolism)

General

Energy
metabolism

Aerobic respiration	Glycolysis → Pyruvate Decarboxylation → Citric acid cycle → Oxidative phosphorylation (Electron Transport Chain + ATP synthase)

Anaerobic respiration	Electron acceptors are other than oxygen

Fermentation	Glycolysis → Substrate-level phosphorylation ABE Ethanol Lactic acid

Specific
paths

Protein metabolism

Carbohydrate metabolism
(Carbohydrate catabolism
and anabolism)

Human

Glycolysis ⇄ Gluconeogenesis

Glycogenolysis ⇄ 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

Amino acid

Nucleotide
metabolism

Other

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

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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

PANDIT:	PF09163
Pseudofam:	PF09163
SCOP:	1kqf
SYSTERS:	Form-deh_trans

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
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

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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 (40)	Full (1298)	Representative proteomes				NCBI (480)	Meta (11)
	Seed (40)	Full (1298)	RP15 (20)	RP35 (52)	RP55 (94)	RP75 (134)	NCBI (480)	Meta (11)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (40)	Full (1298)	Representative proteomes				NCBI (480)	Meta (11)
	Seed (40)	Full (1298)	RP15 (20)	RP35 (52)	RP55 (94)	RP75 (134)	NCBI (480)	Meta (11)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (40)	Full (1298)	Representative proteomes				NCBI (480)	Meta (11)
	Seed (40)	Full (1298)	RP15 (20)	RP35 (52)	RP55 (94)	RP75 (134)	NCBI (480)	Meta (11)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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.

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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

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

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

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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order
family
genus
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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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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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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Form-deh_trans (PF09163)

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Summary: Formate dehydrogenase N, transmembrane

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Formate dehydrogenase Edit Wikipedia article

Contents

Biological function[edit]

Molybdopterin, molybdenum and selenium dependence[edit]

Transmembrane domain[edit]

See also[edit]

References[edit]

External links[edit]

Formate dehydrogenase N, transmembrane Provide feedback

Literature references

External database links

InterPro entry IPR015246

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures