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0  structures 313  species 0  interactions 1703  sequences 21  architectures

Family: Complex1_LYR (PF05347)

Summary: Complex 1 protein (LYR family)

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 "NADH dehydrogenase". More...

NADH dehydrogenase Edit Wikipedia article

NADH dehydrogenase
Identifiers
EC number 1.6.99.3
CAS number 9079-67-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

NADH dehydrogenase (EC 1.6.99.3, cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase) is an enzyme with systematic name NADH:acceptor oxidoreductase.[1][2][3][4] This enzyme catalyses the following chemical reaction

NADH + H+ + acceptor \rightleftharpoons NAD+ + reduced acceptor

NADH dehydrogenase is a flavoprotein that contains iron-sulfur centres.

References

  1. ^ Adachi, K. and Okuyama, T. (1972). "Study on the reduced pyridine nucleotide dehydrogenase of bovine erythrocytes. I. Crystallization and properties of the reduced pyridine nucleotide dehydrogenase of bovine erythrocytes". Biochim. Biophys. Acta 268: 629–637. doi:10.1016/0005-2744(72)90266-5. PMID 4402556. 
  2. ^ Hatefi, Y., Ragan, C.I. and Galante, Y.M. (1985). "The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system". In Martonosi, A. The Enzymes of Biological Membranes 4 (2nd ed.). New York: Plenum Press. pp. 1–70. 
  3. ^ Hochstein, L.I. and Dalton, B.P. (1973). "Studies of a halophilic NADH dehydrogenase. I. Purification and properties of the enzyme". Biochim. Biophys. Acta 302: 216–228. doi:10.1016/0005-2744(73)90150-2. PMID 4144655. 
  4. ^ Kaniuga, Z. (1963). "The transformation of mitochondrial NADH dehydrogenase into NADH:Cytochrome c oxidoreductase". Biochim. Biophys. Acta 73: 550–564. doi:10.1016/0926-6569(63)90175-5. PMID 14074130. 

See also

External links

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.

Complex 1 protein (LYR family) Provide feedback

Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein (Q6Q560) has been shown to play a role in Fe/S cluster biogenesis in mitochondria [1]. We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins.

Literature references

  1. Adam AC, Bornhovd C, Prokisch H, Neupert W, Hell K; , EMBO J. 2006;25:174-183.: The Nfs1 interacting protein Isd11 has an essential role in Fe/S cluster biogenesis in mitochondria. PUBMED:16341090 EPMC:16341090

  2. Wiedemann N, Urzica E, Guiard B, Muller H, Lohaus C, Meyer HE, Ryan MT, Meisinger C, Muhlenhoff U, Lill R, Pfanner N; , EMBO J. 2006;25:184-195.: Essential role of Isd11 in mitochondrial iron-sulfur cluster synthesis on Isu scaffold proteins. PUBMED:16341089 EPMC:16341089


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008011

This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I. The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit SWISSPROT, and the B22 subunit from the human enzyme SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins.

Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.

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 LYR-like (CL0491), which has the following description:

This is a superfamily of sequences with the characteristic LYR, or similar, motif. In some yeasts this family plays a role in Fe-S cluster biogenesis in mitochondria.

The clan contains the following 3 members:

Complex1_LYR Complex1_LYR_1 Complex1_LYR_2

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
(246)
Full
(1703)
Representative proteomes NCBI
(2012)
Meta
(12)
RP15
(377)
RP35
(651)
RP55
(958)
RP75
(1190)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(246)
Full
(1703)
Representative proteomes NCBI
(2012)
Meta
(12)
RP15
(377)
RP35
(651)
RP55
(958)
RP75
(1190)
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
(246)
Full
(1703)
Representative proteomes NCBI
(2012)
Meta
(12)
RP15
(377)
RP35
(651)
RP55
(958)
RP75
(1190)
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: Pfam-B_15215 (release 7.8)
Previous IDs: none
Type: Family
Author: Wood V, Bateman A
Number in seed: 246
Number in full: 1703
Average length of the domain: 60.50 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 42.65 %

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 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 59
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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