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98  structures 836  species 3  interactions 5879  sequences 159  architectures

Family: Cyt-b5 (PF00173)

Summary: Cytochrome b5-like Heme/Steroid binding domain

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This is the Wikipedia entry entitled "Cytochrome b5". More...

Cytochrome b5 Edit Wikipedia article

Cytochrome b5
1jex cyto b5.png
Rat cytochrome b5 bound to heme
Identifiers
Symbol CYB5A
Alt. symbols CYB5
Entrez 1528
HUGO 2570
OMIM 250790
PDB 1JEX (RCSB PDB PDBe PDBj)
RefSeq NM_001914
UniProt P00167
Other data
Locus Chr. 18 q23
Cytochrome b5
Identifiers
Symbol Cyt_B5
Pfam PF00173
InterPro IPR001199
PROSITE PDOC00170

Cytochromes b5 are ubiquitous electron transport hemoproteins found in animals, plants, fungi and purple phototrophic bacteria. The microsomal and mitochondrial variants are membrane-bound, while bacterial and those from erythrocytes and other animal tissues are water-soluble. The family of cytochrome b5-like proteins includes (besides cytochrome b5 itself) hemoprotein domains covalently associated with other redox domains in flavocytochrome cytochrome b2 (L-lactate dehydrogenase; EC 1.1.2.3), sulfite oxidase (EC 1.8.3.1), plant and fungal nitrate reductases (EC 1.7.1.1, EC 1.7.1.2, EC 1.7.1.3), and plant and fungal cytochrome b5/acyl lipid desaturase fusion proteins.

Structure[edit]

3-D structures of a number of cytochrome b5 and yeast flavocytochrome b2 are known. The fold belongs to the α+β class, with two hydrophobic cores on each side of a β-sheet. The larger hydrophobic core constitutes the heme-binding pocket, closed off on each side by a pair of helices connected by a turn. The smaller hydrophobic core may have only a structural role and is formed by spatially close N-terminal and C-terminal segments. The two histidine residues provide the fifth and sixth heme ligands, and the propionate edge of the heme group lies at the opening of the heme crevice. Two isomers of cytochrome b5, referred to as the A (major) and B (minor) forms, differ by a 180° rotation of the heme about an axis defined by the α- and γ-meso carbons.

Cytochrome b5 in some biochemical reactions[edit]

EC 1.6.2.2 cytochrome-b5 reductase

NADH + H+ + 2 ferricytochrome b5 → NAD+ + 2 ferrocytochrome b5

EC 1.10.2.1 L-ascorbate—cytochrome-b5 reductase

L-ascorbate + ferricytochrome b5 → monodehydroascorbate + ferrocytochrome b5

EC 1.14.18.2 CMP-N-acetylneuraminate monooxygenase

CMP-N-acetylneuraminate + 2 ferrocytochrome b5 + O2 + 2 H+ → CMP-N-glycoloylneuraminate + 2 ferricytochrome b5 + H2O

EC 1.14.19.1 stearoyl-CoA 9-desaturase

stearoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ → oleoyl-CoA + 2 ferricytochrome b5 + H2O

EC 1.14.19.3 linoleoyl-CoA 9-desaturase

linoleoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ → γ-linolenoyl-CoA + 2 ferricytochrome b5 + H2O

See also[edit]

References[edit]

  • Lederer, F. (1994). "The cytochrome b5-fold: an adaptable module". Biochimie 76 (7): 674–692. doi:10.1016/0300-9084(94)90144-9. PMID 7893819. 
  • Napier, J.A., Michaelson, L.V. and Sayanova, O. (2003). "The role of cytochrome b5 fusion desaturases in the synthesis of polyunsaturated fatty acids". Prostaglandins, Leukotrienes and Essential Fatty Acids 68 (2): 135–143. doi:10.1016/S0952-3278(02)00263-6. PMID 12538077. 
  • Rivera, M., Barillas-Mury, C., Christensen, K.A., Little, J.W., Wells, M.A. and Walker, F.A. (1992). "Gene synthesis, bacterial expression, and 1H NMR spectroscopic studies of the rat outer mitochondrial membrane cytochrome b5". Biochemistry 31 (48): 12233–12240. doi:10.1021/bi00163a037. PMID 1333795. 
  • Schenkman, J.B. and Jansson, I. (2003). "The many roles of cytochrome b5". Pharmacol. Ther. 97 (2): 139–152. doi:10.1016/S0163-7258(02)00327-3. PMID 12559387. 

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.

Cytochrome b5-like Heme/Steroid binding domain Provide feedback

This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as O00264 [1,2]. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.

Literature references

  1. Gerdes D, Wehling M, Leube B, Falkenstein E; , Biol Chem 1998;379:907-911.: Cloning and tissue expression of two putative steroid membrane receptors. PUBMED:9705155 EPMC:9705155

  2. Meyer C, Schmid R, Scriba PC, Wehling M; , Eur J Biochem 1996;239:726-731.: Purification and partial sequencing of high-affinity progesterone-binding site(s) from porcine liver membranes. PUBMED:8774719 EPMC:8774719

  3. Mifsud W, Bateman A; , Genome Biol 2002;3:0-0.: Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain. PUBMED:12537557 EPMC:12537557


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001199

Cytochromes b5 are ubiquitous electron transport proteins found in animals, plants and yeasts [PUBMED:2752049]. The microsomal and mitochondrial variants are membrane-bound, while those from erythrocytes and other animal tissues are water-soluble [PUBMED:4030743, PUBMED:8439576].

The 3D structure of bovine cyt b5 is known, the fold belonging to the alpha+beta class, with 5 strands and 5 short helices forming a framework for supporting a central haem group [PUBMED:1167544]. The cytochrome b5 domain is similar to that of a number of oxidoreductases, such as plant and fungal nitrate reductases, sulphite oxidase, yeast flavocytochrome b2 (L-lactate dehydrogenase) and plant cyt b5/acyl lipid desaturase fusion protein.

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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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...

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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
(210)
Full
(5879)
Representative proteomes NCBI
(5749)
Meta
(252)
RP15
(1318)
RP35
(2157)
RP55
(3127)
RP75
(3763)
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Format an alignment

  Seed
(210)
Full
(5879)
Representative proteomes NCBI
(5749)
Meta
(252)
RP15
(1318)
RP35
(2157)
RP55
(3127)
RP75
(3763)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(210)
Full
(5879)
Representative proteomes NCBI
(5749)
Meta
(252)
RP15
(1318)
RP35
(2157)
RP55
(3127)
RP75
(3763)
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.

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: Bateman A
Previous IDs: heme_1;
Type: Domain
Author: Bateman A
Number in seed: 210
Number in full: 5879
Average length of the domain: 82.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 17.81 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 76
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Cyt-b5 Oxidored_molyb FMN_dh

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 Cyt-b5 domain has been found. There are 98 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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