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4  structures 42  species 2  interactions 50  sequences 5  architectures

Family: Dehyd-heme_bind (PF09098)

Summary: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding

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Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding Provide feedback

Members of this family are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase. They have a predominantly alpha-helical structure and can be divided into two subdomains, each binding a haem C group via a conserved CXXCH motif [1,2].

Literature references

  1. Datta S, Ikeda T, Kano K, Mathews FS; , Acta Crystallogr D Biol Crystallogr. 2003;59:1551-1556.: Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. PUBMED:12925784 EPMC:12925784

  2. Satoh A, Kim JK, Miyahara I, Devreese B, Vandenberghe I, Hacisalihoglu A, Okajima T, Kuroda S, Adachi O, Duine JA, Van Beeumen J, Tanizawa K, Hirotsu K; , J Biol Chem. 2002;277:2830-2834.: Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges. PUBMED:11704672 EPMC:11704672


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015182

Quinohemoprotein amine dehydrogenases (QHNDH) EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms [PUBMED:15234267]. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue [PUBMED:12925784]. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [PUBMED:12974623, PUBMED:12427036].

QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends [PUBMED:11704672].

This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem [PUBMED:12925784].

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 Cytochrome-c (CL0318), which has the following description:

This family includes proteins where a covalently-bound haem completes the core. The core is three helices in an open folded leaf formation. The members are monodomain cytochromes.

The clan contains the following 10 members:

CCP_MauG Cytochrom_C Cytochrom_C1 Cytochrom_C550 Cytochrome_CBB3 Dehyd-heme_bind DUF1111 DUF1924 FixO PSCyt1

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
(11)
Full
(50)
Representative proteomes NCBI
(60)
Meta
(5)
RP15
(3)
RP35
(13)
RP55
(16)
RP75
(19)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(11)
Full
(50)
Representative proteomes NCBI
(60)
Meta
(5)
RP15
(3)
RP35
(13)
RP55
(16)
RP75
(19)
Alignment:
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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
(11)
Full
(50)
Representative proteomes NCBI
(60)
Meta
(5)
RP15
(3)
RP35
(13)
RP55
(16)
RP75
(19)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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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: pdb_1pby
Previous IDs: none
Type: Domain
Author: Sammut SJ, Eberhardt R
Number in seed: 11
Number in full: 50
Average length of the domain: 135.40 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 33.92 %

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 25.2 25.2
Trusted cut-off 25.3 25.4
Noise cut-off 25.1 25.1
Model length: 167
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Qn_am_d_aIV QH-AmDH_gamma

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 Dehyd-heme_bind domain has been found. There are 4 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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