Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
228  structures 8786  species 0  interactions 20589  sequences 93  architectures

Family: NAD_synthase (PF02540)

Summary: NAD synthase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

NAD synthase Provide feedback

NAD synthase ( EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.

Literature references

  1. Rizzi M, Nessi C, Mattevi A, Coda A, Bolognesi M, Galizzi A; , EMBO J 1996;15:5125-5134.: Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis. PUBMED:8895556 EPMC:8895556


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022310

NAD+ synthase ( EC ) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology [ PUBMED:8895556 ].

This domain is also found in guanosine 5'-monophosphate (GMP) synthetase. GMP synthase catalyses the synthesis of GMP from XMP. The protein is a homodimer, but in some archaea it is a heterodimer composed of a glutamine amidotransferase subunit and a ATP pyrophosphatase subunit. In eucaryotes, bacteria, and some archaea the two catalytic units are encoded by a single gene, producing a two-domain-type GMP, with a GATase domain in the N-terminal half and a ATP-PPase domain in the C-terminal half. This entry represents the ATP pyrophosphatase domain.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan HUP (CL0039), which has the following description:

The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase named after the ATP PyroPhosphatase domain, was initially identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily contains USPA, ETFP and Photolyases [1]

The clan contains the following 32 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 BshC CDPS Citrate_ly_lig CTP_transf_like Diphthami_syn_2 DNA_photolyase DPRP ETF FAD_syn HIGH_NTase1 HIGH_NTase1_ass NAD_synthase Pantoate_ligase PAPS_reduct QueC QueH ThiI tRNA-synt_1 tRNA-synt_1_2 tRNA-synt_1b tRNA-synt_1c tRNA-synt_1d tRNA-synt_1e tRNA-synt_1f tRNA-synt_1g tRNA_Me_trans UDPG_MGDP_dh_C Usp

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(9)
Full
(20589)
Representative proteomes UniProt
(95741)
RP15
(3066)
RP35
(10043)
RP55
(20490)
RP75
(34349)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(9)
Full
(20589)
Representative proteomes UniProt
(95741)
RP15
(3066)
RP35
(10043)
RP55
(20490)
RP75
(34349)
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
(9)
Full
(20589)
Representative proteomes UniProt
(95741)
RP15
(3066)
RP35
(10043)
RP55
(20490)
RP75
(34349)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: COGs
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 9
Number in full: 20589
Average length of the domain: 179.80 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 35.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 242
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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_synthase domain has been found. There are 228 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 sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R4IPE7 View 3D Structure Click here
A0A1D6EKN6 View 3D Structure Click here
A4I7Y2 View 3D Structure Click here
B8JLW8 View 3D Structure Click here
I1K669 View 3D Structure Click here
I1KPN4 View 3D Structure Click here
O74940 View 3D Structure Click here
P04079 View 3D Structure Click here
P18843 View 3D Structure Click here
P32073 View 3D Structure Click here
P38625 View 3D Structure Click here
P38795 View 3D Structure Click here
P49915 View 3D Structure Click here
P9WJJ3 View 3D Structure Click here
P9WMS7 View 3D Structure Click here
Q09580 View 3D Structure Click here
Q0D8D4 View 3D Structure Click here
Q2G236 View 3D Structure Click here
Q3THK7 View 3D Structure Click here
Q4CPU6 View 3D Structure Click here
Q4D8M8 View 3D Structure Click here
Q4V7C6 View 3D Structure Click here
Q54ML1 View 3D Structure Click here
Q58531 View 3D Structure Click here
Q58747 View 3D Structure Click here
Q59032 View 3D Structure Click here
Q5ALW6 View 3D Structure Click here
Q5APF2 View 3D Structure Click here
Q6IA69 View 3D Structure Click here
Q711T7 View 3D Structure Click here
Q812E8 View 3D Structure Click here
Q8I2P2 View 3D Structure Click here
Q8IJR9 View 3D Structure Click here
Q9C723 View 3D Structure Click here
Q9CAD1 View 3D Structure Click here
Q9VIE7 View 3D Structure Click here
Q9VYA0 View 3D Structure Click here
Q9XXK6 View 3D Structure Click here