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15  structures 3181  species 0  interactions 5590  sequences 89  architectures

# Summary: Respiratory-chain NADH dehydrogenase 51 Kd subunit

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...

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. 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. PMID 4144655.
4. ^ Kaniuga, Z. (1963). "The transformation of mitochondrial NADH dehydrogenase into NADH:Cytochrome c oxidoreductase". Biochim. Biophys. Acta 73: 550–564. PMID 14074130.

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.

# Respiratory-chain NADH dehydrogenase 51 Kd subunit

No Pfam abstract.

This tab holds annotation information from the InterPro database.

# InterPro entry IPR011538

NADH:ubiquinone oxidoreductase (complex I) (EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [PUBMED:1470679]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [PUBMED:10940377], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [PUBMED:18394423]. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters [PUBMED:18563446]. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [PUBMED:18563446, PUBMED:17854760]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I [PUBMED:18982432].

Thie entry represents the 51 kDa subunit from NADH:ubiquinone oxidoreductase [PUBMED:2029890]. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 51 kDa (in mammals), which is the second largest subunit of complex I and is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind to NAD, FMN, and a 2Fe-2S cluster. The 51 kDa subunit and the bacterial hydrogenase alpha subunit contain three regions of sequence similarities. The first one most probably corresponds to the NAD-binding site, the second to the FMN-binding site, and the third one, which contains three cysteines, to the iron-sulphur binding region.

### 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...

# Pfam Clan

This family is a member of clan Hybrid (CL0105), which has the following description:

This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.

The clan contains the following 17 members:

Complex1_51K

# 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...

## 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
(123)
Full
(5590)
Representative proteomes NCBI
(4537)
Meta
(2950)
RP15
(615)
RP35
(1120)
RP55
(1387)
RP75
(1614)
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HTML View    View  View  View  View
PP/heatmap 1   View  View  View  View
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, not available.

## Format an alignment

Seed
(123)
Full
(5590)
Representative proteomes NCBI
(4537)
Meta
(2950)
RP15
(615)
RP35
(1120)
RP55
(1387)
RP75
(1614)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(123)
Full
(5590)
Representative proteomes NCBI
(4537)
Meta
(2950)
RP15
(615)
RP35
(1120)
RP55
(1387)
RP75
(1614)

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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.

# 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

 Seed source: Pfam-B_780 (release 4.0) Previous IDs: none Type: Family Author: Bateman A Number in seed: 123 Number in full: 5590 Average length of the domain: 161.60 aa Average identity of full alignment: 39 % Average coverage of the sequence by the domain: 31.64 %

## HMM information

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 20.5 20.5
Trusted cut-off 20.8 20.5
Noise cut-off 20.4 20.3
Model length: 151
Family (HMM) version: 12

# Species distribution

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