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27  structures 2140  species 0  interactions 2429  sequences 22  architectures

Family: PNTB (PF02233)

Summary: NAD(P) transhydrogenase beta subunit

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NAD(P) transhydrogenase beta subunit Provide feedback

This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes. The domain is often found in conjunction with PF01262. Pyridine nucleotide transhydrogenase catalyses the reduction of NAD+ to NADPH. A complete loss of activity occurs upon mutation of Gly314 in E. coli [1].

Literature references

  1. Ahmad S, Glavas NA, Bragg PD; , Eur J Biochem 1992;207:733-739.: A mutation at Gly314 of the beta subunit of the Escherichia coli pyridine nucleotide transhydrogenase abolishes activity and affects the NADP(H)-induced conformational change. PUBMED:1633824 EPMC:1633824


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012136

NAD(P) transhydrogenase catalyses the transfer of reducing equivalents between NAD(H) and NADP(H), coupled to the translocation of protons across a membrane [PUBMED:12788487]. It is an integral membrane protein found in most organisms except for yeasts, plants and some bacterial species. In bacterial species it is located in the cytoplasmic membrane, while in mitochondria it is located in the inner membrane. Under most physiological conditions this enzyme synthesises NADPH, driven by consumption of the proton electrochemical gradient. The resulting NADPH is subsequently used for biosynthetic reactions or the reduction of glutathione.

The global structure of this enzyme is similar in all organisms, consisting of three distinct domains, though the polypeptide composition can vary. Domain I binds NAD(+)/NADH, domain II is a hydrophobic membrane-spanning domain, and domain III binds NADP(+)/NADPH. Domain I is composed of two subdomains, both of which form a Rossman fold, while domain III consists of a single Rossman fold where the NADP(+) is flipped relative to the normal orientation of bound nucleotides within the Rossman fold [PUBMED:10997900, PUBMED:11004437, PUBMED:12791694]. Several residues within these domains are thought to make functionally important interdomain contacts for hydride transfer between these domains [PUBMED:11250201]. Proton translocation occurs through domain II and is thought to induce conformational changes which are transmitted across domain III to the site of hydride transfer between domains I and III.

This entry represents the beta subunit found in bacterial two-subunit NADP(H) transhydrogenases. This subunit forms domain III and part of the transmembrane domain II.

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 FAD_DHS (CL0085), which has the following description:

The members of this family adopt a Rossmann fold, similar to CLAN:CL0063. However, the members of this family are distinguished in that the FAD/NAD cofactor is bound in the opposite direction. In this arrangement, the adenosine moiety is found bound at the second half of the fold. In addition, the conserved GxGxxG motif found in classical NADP binding Rossmann folds is absent. Finally, another distinguishing characteristic is the formation of an internal hydrogen bond in the FAD molecule [1].

The clan contains the following 7 members:

CO_dh DS ETF_alpha PNTB SIR2 SIR2_2 TPP_enzyme_M

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.

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(10)
Full
(2429)
Representative proteomes NCBI
(1732)
Meta
(3888)
RP15
(215)
RP35
(421)
RP55
(584)
RP75
(707)
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Format an alignment

  Seed
(10)
Full
(2429)
Representative proteomes NCBI
(1732)
Meta
(3888)
RP15
(215)
RP35
(421)
RP55
(584)
RP75
(707)
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
(10)
Full
(2429)
Representative proteomes NCBI
(1732)
Meta
(3888)
RP15
(215)
RP35
(421)
RP55
(584)
RP75
(707)
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_2220 (release 5.2)
Previous IDs: none
Type: Family
Author: Bateman A, Mian N
Number in seed: 10
Number in full: 2429
Average length of the domain: 439.00 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 87.05 %

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 19.8 19.8
Trusted cut-off 19.8 20.2
Noise cut-off 19.7 19.7
Model length: 464
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 PNTB domain has been found. There are 27 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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