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116  structures 5730  species 0  interactions 11049  sequences 43  architectures

Family: Sdh_cyt (PF01127)

Summary: Succinate dehydrogenase/Fumarate reductase transmembrane subunit

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This is the Wikipedia entry entitled "Fumarate reductase". More...

Fumarate reductase Edit Wikipedia article

Fumarate reductase is the enzyme that converts fumarate to succinate.

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 "Succinate dehydrogenase". More...

Succinate dehydrogenase Edit Wikipedia article

Succinate - coenzyme Q reductase also called succinate dehydrogenase is an enzyme complex found in the matrix part of the inner mitochondrial membrane. The enzyme complex has two main parts where one is part of both the citric acid cycle with the task of converting succinate into fumarate and the other is complex II of the electron transport chain, which uses electrons freed from succinate, to reduce ubiquinone to ubiquinol, ubiquinol is the input of the next complex in the electron transport chain, complex III, coenzyme Q - cytochrome c reductase.

In the citric acid cycle succinate is oxidized by the succinate dehydrogenase part of the complex and 2e- + 2H+ is transferred from succinate to FAD, a coenzyme which is covalently attached to a histidine residue in the enzyme. FADH2, the reduced form of FAD, will then transfer the two electrons to iron-sulfur clusters inside the enzyme and release the 2H+ back into the micochondrial matrix. The iron-sulfur clusters will reduce ubiquinone, Q, to ubiquinol, QH2.

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.

Succinate dehydrogenase/Fumarate reductase transmembrane subunit Provide feedback

This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.

Literature references

  1. Lancaster CR, Kroger A, Auer M, Michel H; , Nature 1999;402:377-385.: Structure of fumarate reductase from Wolinella succinogenes at 2.2 A resolution. PUBMED:10586875 EPMC:10586875


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000701

Succinate dehydrogenase (SDH) is a membrane-bound complex of two main components: a membrane-extrinsic component composed of an FAD-binding flavoprotein and an iron-sulphur protein, and a hydrophobic component composed of a cytochrome b and a membrane anchor protein. The cytochrome b component is a mono-haem transmembrane protein [ PUBMED:1447196 , PUBMED:8152421 , PUBMED:7616569 ] belonging to a family that includes:

  • Cytochrome b-556 from bacterial SDH (gene sdhC).
  • Cytochrome b560 from the mammalian mitochondrial SDH complex, which is encoded in the mitochondrial genome of some algae and in the plant Marchantia polymorpha.
  • Cytochrome b from yeast mitochondrial SDH complex (gene SDH3 or CYB3).
  • Protein cyt-1 from Caenorhabditis elegans.

These cytochromes are proteins of about 130 residues that comprise three transmembrane regions. There are two conserved histidines which may be involved in binding the haem group.

This family also includes the subunit C (the cytochrome B subunit) of type B fumarate reductases [ PUBMED:9210286 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan FumRed-TM (CL0335), which has the following description:

This superfamily constitutes two distinct families: in one family the common fold is contained in a single-chain subunit, in the other it is formed by two chains.

The clan contains the following 5 members:

CybS Fumarate_red_C Fumarate_red_D MCP1_TM Sdh_cyt

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 and the UniProtKB sequence database. More...

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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
(59)
Full
(11049)
Representative proteomes UniProt
(44833)
RP15
(1368)
RP35
(5028)
RP55
(10977)
RP75
(19070)
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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
(59)
Full
(11049)
Representative proteomes UniProt
(44833)
RP15
(1368)
RP35
(5028)
RP55
(10977)
RP75
(19070)
Alignment:
Format:
Order:
Sequence:
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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
(59)
Full
(11049)
Representative proteomes UniProt
(44833)
RP15
(1368)
RP35
(5028)
RP55
(10977)
RP75
(19070)
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: Prosite & Structural domain
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 59
Number in full: 11049
Average length of the domain: 116.6 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 75.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.8 25.8
Trusted cut-off 25.8 25.8
Noise cut-off 25.7 25.7
Model length: 121
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Selections

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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 Sdh_cyt domain has been found. There are 116 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077YWQ6 View 3D Structure Click here
A0A0D2F051 View 3D Structure Click here
A0A0D2FEP3 View 3D Structure Click here
A0A0H3GQ10 View 3D Structure Click here
A0A0K0EJQ3 View 3D Structure Click here
A0A0K0JJQ0 View 3D Structure Click here
A0A0N4U1F3 View 3D Structure Click here
A0A158N8N8 View 3D Structure Click here
A0A175VX16 View 3D Structure Click here
A0A1C1CN74 View 3D Structure Click here
A0A1C1CVZ9 View 3D Structure Click here
A0A3P7ED17 View 3D Structure Click here
B0S5Q2 View 3D Structure Click here
B6SHQ2 View 3D Structure Click here
B6SIX4 View 3D Structure Click here
C0NJ76 View 3D Structure Click here
C0NTU4 View 3D Structure Click here
C1H0D8 View 3D Structure Click here
C6SVE8 View 3D Structure Click here
D0VWV4 View 3D Structure Click here
G4V7H1 View 3D Structure Click here
I1KFD0 View 3D Structure Click here
K0ENQ2 View 3D Structure Click here
K0ETN9 View 3D Structure Click here
O06912 View 3D Structure Click here
O29573 View 3D Structure Click here
O53368 View 3D Structure Click here
O53369 View 3D Structure Click here
O74882 View 3D Structure Click here
P08064 View 3D Structure Click here
P0DKI0 View 3D Structure Click here
P0DKI1 View 3D Structure Click here
P17413 View 3D Structure Click here
P33421 View 3D Structure Click here
P35720 View 3D Structure Click here
P41085 View 3D Structure Click here
P41086 View 3D Structure Click here
P41955 View 3D Structure Click here
P41956 View 3D Structure Click here
P51055 View 3D Structure Click here