Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
18  structures 1966  species 7  interactions 10033  sequences 66  architectures

Family: Proton_antipo_M (PF00361)

Summary: Proton-conducting membrane transporter

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Membrane transport protein". More...

Membrane transport protein Edit Wikipedia article

A membrane transport protein (or simply transporter) is a membrane protein[1] involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane. Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport. The two main types of proteins involved in such transport are broadly categorized as either channels or carriers.

Difference between channels and carriers

A carrier is not open simultaneously to the both environment (extracellular and intracellular). Either its inner gate is open, or outer gate is open. Carriers have binding sites, but pores and channels do not. When a channel is opened, thousands to millions of ions can pass through the membrane in one time, but only one or a small amount of molecules can pass through a carrier molecule.[2][3][4] Each carrier protein is designed to recognize only one substance or one group of very similar substances. Research has correlated defects in specific carrier proteins with specific diseases.[5]

Active transport

Main article: Active transport
The action of the sodium-potassium pump is an example of primary active transport. The two carrier proteins on the left are using ATP to move sodium out of the cell against the concentration gradient. The proteins on the right are using secondary active transport to move potassium into the cell.

Active transport is the movement of a substance across a membrane against its concentration gradient. This is usually to accumulate high concentrations of molecules that a cell needs, such as glucose or amino acids. When the lipid bilayer is impermeable to the molecule needing transport, active transport is also necessary. If the process uses chemical energy, such as adenosine triphosphate (ATP), it is called primary active transport. Secondary active transport involves the use of an electrochemical gradient, and does not use energy produced in the cell.[6] Unlike channel proteins which only transport substances through membranes passively, carrier proteins can transport ions and molecules either passively through facilitated diffusion, or via secondary active transport.[7] A carrier protein is required to move particles from areas of low concentration to areas of high concentration. These carrier proteins have receptors that bind to a specific molecule (substrate) needing transport. The molecule or ion to be transported (the substrate) must first bind at a binding site at the carrier molecule, with a certain binding affinity. Following binding, and while the binding site is facing the same way, the carrier will capture or occlude (take in and retain) the substrate within its molecular structure and cause an internal translocation so that the opening in the protein now faces the other side of the plasma membrane.[8] The carrier protein substrate is released at that site, according to its binding affinity there.

Facilitated diffusion

Main article: Facilitated diffusion
Facilitated diffusion in cell membrane, showing ion channels (left) and carrier proteins (three on the right).

Facilitated diffusion is the passage of molecules or ions across a biological membrane through specific transport proteins and requires no energy input. Facilitated diffusion is used especially in the case of large polar molecules and charged ions; once such ions are dissolved in water they cannot diffuse freely across cell membranes due to the hydrophobic nature of the fatty acid tails of the phospholipids that make up the bilayers. The type of carrier proteins used in facilitated diffusion is slightly different from those used in active transport. They are still transmembrane carrier proteins, but these are gated transmembrane channels, meaning they do not internally translocate, nor require ATP to function. The substrate is taken in one side of the gated carrier, and without using ATP the substrate is released into the cell. They may be used as potential biomarkers

Types

(Grouped by Transporter Classification database categories)

1: Channels/pores

Facilitated diffusion occurs in and out of the cell membrane via channels/pores and carriers/porters.

Note:

  • Channels:

Channels are either in open state or closed state. When a channel is opened with a slight conformational switch, it is open to both environment simultaneously (extracellular and intracellular)

  • Pores:

Pores are continuously open to these both environment, because they do not undergo conformational changes. They are always open and active.

2: Electrochemical potential-driven transporters

3: Primary active transporters

4: Group translocators

The group translocators provide a special mechanism for the phosphorylation of sugars as they are transported into bacteria (PEP group translocation)

5: Electron carriers

The transmembrane electron transfer carriers in the membrane include two-electron carriers, such as the disulfide bond oxidoreductases (DsbB and DsbD in E. coli) as well as one-electron carriers such as NADPH oxidase. Often these redox proteins are not considered transport proteins.

Examples

Each carrier protein, even within the same cell membrane, is specific to one type or family of molecules. For example, GLUT1 is a named carrier protein found in almost all animal cell membranes that transports glucose across the bilayer. Other specific carrier proteins also help the body function in important ways. Cytochromes operate in the electron transport chain as carrier proteins for electrons.[6]

Pathology

A number of inherited diseases involve defects in carrier proteins in a particular substance or group of cells. Cysteinuria (cysteine in the urine and the bladder) is such a disease involving defective cysteine carrier proteins in the kidney cell membranes. This transport system normally removes cysteine from the fluid destined to become urine and returns this essential amino acid to the blood. When this carrier malfunctions, large quantities of cysteine remain in the urine, where it is relatively insoluble and tends to precipitate. This is one cause of urinary stones.[9] Some vitamin carrier proteins have been shown to be overexpressed in patients with malignant disease. For example, levels of riboflavin carrier protein (RCP) have been shown to be significantly elevated in people with breast cancer.[10]

See also

References

  1. ^ Membrane transport proteins at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ Sadava, David, et al. Life, the Science of Biology, 9th Edition. Macmillan Publishers, 2009. ISBN 1-4292-1962-9. p. 119.
  3. ^ Cooper, Geoffrey (2009). The Cell: A Molecular Approach. Washington, DC: ASM Press. p. 62. ISBN 9780878933006. 
  4. ^ Thompson, Liz A. Passing the North Carolina End of Course Test for Biology. American Book Company, Inc. 2007. ISBN 1-59807-139-4. p. 97.
  5. ^ Sadava, David, Et al. Life, the Science of Biology, 9th Edition. Macmillan Publishers, 2009. ISBN 1-4292-1962-9. p. 119.
  6. ^ a b Ashley, Ruth. Hann, Gary. Han, Seong S. Cell Biology. New Age International Publishers. ISBN 8122413978. p. 113.
  7. ^ Taiz, Lincoln. Zeigler, Eduardo. Plant Physiology and Development. Sinauer Associates, 2015. ISBN 978-1-60535-255-8. pp. 151.
  8. ^ Kent, Michael. Advanced Biology. Oxford University Press US, 2000. ISBN 0-19-914195-9. pp. 157–158.
  9. ^ Sherwood, Lauralee. 7th Edition. Human Physiology. From Cells to Systems. Cengage Learning, 2008. p. 67
  10. ^ Rao, PN, Levine, E et al. Elevation of Serum Riboflavin Carrier Protein in Breast Cancer. Cancer Epidemiol Biomarkers Prev. Volume 8 No 11. pp. 985–990

External links

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

This is the Wikipedia entry entitled "NADH dehydrogenase (ubiquinone)". More...

NADH dehydrogenase (ubiquinone) Edit Wikipedia article

  • This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name. For more information follow the bold category link.

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.

Proton-conducting membrane transporter Provide feedback

This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2]. The family in total represents homologues across the phyla.

Literature references

  1. Walker JE; , Q Rev Biophys 1992;25:253-324.: The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. PUBMED:1470679 EPMC:1470679

  2. Morino M, Suzuki T, Ito M, Krulwich TA;, J Bacteriol. 2014;196:28-35.: Purification and functional reconstitution of a seven-subunit mrp-type na+/h+ antiporter. PUBMED:24142251 EPMC:24142251


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001750

This domain is found in subunits NuoL/ND5, NuoM/ND4, and NuoN/ND2 of the NADH:quinone oxidoreductase (complex I), Mrp antiporters subunits A and D, and in membrane subunits of hydrogenase complexes, such as hydrogenase-4 and F420H2 dehydrogenase.

Mrp-type antiporters comprise the cation/proton antiporter family 3 (CPA3), commonly referred to as Mrp. They are the products of operons that carry either six or seven genes (mrpA-G), and form complexes containing all subunits [PUBMED:15980940, PUBMED:18408029]. They have Na(+)/H(+) antiporter activity [PUBMED:24142251]. Two of the Mrp proteins, MrpA and MrpD, resemble NuoL/ND5, NuoM/ND4, NuoN/ND2, the homologous subunits that constitute the membrane-embedded, proton-translocating core of complex I [PUBMED:12914915, PUBMED:20826797, PUBMED:12460669, PUBMED:20595580]. They also resemble subunits of membrane-bound hydrogenases, such as HyfB, HyfD and HyfF from E.coli [PUBMED:9387241] and F420H2 dehydrogenasa (FPO complex) subunits L, N and M [PUBMED:10751389].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan ComplexI-N (CL0425), which has the following description:

This superfamily contains proteins from the families Oxidored_q1 and NADHdeh_related. The Oxidored_q1 family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. Many members of the NADHdeh_related family are archaeal and bacterial, indicating the evolutionary origins of ComplexI.

The clan contains the following 2 members:

NADHdeh_related Proton_antipo_M

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...

View options

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
(14)
Full
(10033)
Representative proteomes UniProt
(169814)
NCBI
(185138)
Meta
(9923)
RP15
(2583)
RP35
(7689)
RP55
(13207)
RP75
(20420)
Jalview View  View  View  View  View  View  View  View  View 
HTML View                 
PP/heatmap 1                

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(14)
Full
(10033)
Representative proteomes UniProt
(169814)
NCBI
(185138)
Meta
(9923)
RP15
(2583)
RP35
(7689)
RP55
(13207)
RP75
(20420)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(14)
Full
(10033)
Representative proteomes UniProt
(169814)
NCBI
(185138)
Meta
(9923)
RP15
(2583)
RP35
(7689)
RP55
(13207)
RP75
(20420)
Raw Stockholm Download   Download   Download   Download   Download   Download       Download  
Gzipped 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.

HMM logo

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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: Pfam-B_4 (release 1.0)
Previous IDs: oxidored_q1; Oxidored_q1;
Type: Family
Author: Finn RD, Eberhardt R
Number in seed: 14
Number in full: 10033
Average length of the domain: 279.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 51.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.1 21.4
Model length: 293
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 7 interactions for this family. More...

Oxidored_q2 Oxidored_q4 Oxidored_q2 Oxidored_q3 Proton_antipo_M Proton_antipo_N Oxidored_q3

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 Proton_antipo_M domain has been found. There are 18 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...