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191  structures 4712  species 7  interactions 19747  sequences 239  architectures

Family: NAD_binding_1 (PF00175)

Summary: Oxidoreductase NAD-binding domain

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This is the Wikipedia entry entitled "Oxidoreductase NAD-binding domain". More...

Oxidoreductase NAD-binding domain Edit Wikipedia article

Oxidoreductase NAD-binding domain
Identifiers
Symbol NAD_binding_1
Pfam PF00175
InterPro IPR001433
SCOP 2cnd
SUPERFAMILY 2cnd
TCDB 3.D.5

Oxidoreductase NAD-binding domain is an evolutionary conserved protein domain.[1]

Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.

Bacterial ferredoxin-NADP+ reductase may be bound to the thylakoid membrane or anchored to the thylakoid-bound phycobilisomes. Chloroplast ferredoxin-NADP+ reductase (EC 1.18.1.2) may play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power. It is involved in the final step in the linear photosynthetic electron transport chain and has also been implicated in cyclic electron flow around photosystem I where its role would be to return electrons from ferredoxin to the cytochrome B-F complex.

This domain is present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase and others.

Examples[edit]

Human genes encoding proteins containing this domain include:

References[edit]

  1. ^ Hyde GE, Crawford NM, Campbell WH (December 1991). "The sequence of squash NADH:nitrate reductase and its relationship to the sequences of other flavoprotein oxidoreductases. A family of flavoprotein pyridine nucleotide cytochrome reductases". J. Biol. Chem. 266 (35): 23542–7. PMID 1748631. 

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Oxidoreductase NAD-binding domain Provide feedback

Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.

Literature references

  1. Hyde GE, Crawford NM, Campbell W; , J Biol Chem 1991;266:23542-23547.: The sequence of squash NADH:nitrate reductase and its relationship to the sequences of other flavoprotein oxidoreductases. A family of flavoprotein pyridine nucleotide cytochrome reductases. PUBMED:1748631 EPMC:1748631


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001433

Bacterial ferredoxin-NADP+ reductase may be bound to the thylakoid membrane or anchored to the thylakoid-bound phycobilisomes. Chloroplast ferredoxin-NADP+ reductase (EC) may play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power. It is involved in the final step in the linear photosynthetic electron transport chain and has also been implicated in cyclic electron flow around photosystem I where its role would be to return electrons from ferredoxin to the cytochrome B-F complex.

This domain is present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase, as well as others.

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 NAD_Ferredoxin (CL0091), which has the following description:

The Ferredoxin / Ferric reductase-like NAD binding domain is adopts a Rossmann like fold. However, these families have been excluded from the classical NAD(P) binding Rossmann clan (CLAN:CL0063), due to a divergence of the GxGxxG motif. In this clan, the motif phosphate binding motif is G-T/S-G-A/I-P. The changes in the motif are a reflection of the different way that the NAD(P)H is bound by this fold and the classical Rossmann fold [1,2].

The clan contains the following 2 members:

NAD_binding_1 NAD_binding_6

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
(72)
Full
(19747)
Representative proteomes NCBI
(15837)
Meta
(2129)
RP15
(1691)
RP35
(3423)
RP55
(4899)
RP75
(6047)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(72)
Full
(19747)
Representative proteomes NCBI
(15837)
Meta
(2129)
RP15
(1691)
RP35
(3423)
RP55
(4899)
RP75
(6047)
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
(72)
Full
(19747)
Representative proteomes NCBI
(15837)
Meta
(2129)
RP15
(1691)
RP35
(3423)
RP55
(4899)
RP75
(6047)
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: Prosite
Previous IDs: oxidored_fad; NAD_binding;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 72
Number in full: 19747
Average length of the domain: 105.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 24.44 %

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 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 109
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 7 interactions for this family. More...

NAD_binding_1 Flavodoxin_1 Fer2 Globin FAD_binding_1 FAD_binding_6 DHODB_Fe-S_bind

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 NAD_binding_1 domain has been found. There are 191 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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