Summary: FAD synthetase

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Wikipedia: Prokaryotic riboflavin biosynthesis protein
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Prokaryotic riboflavin biosynthesis protein

FAD synthetase

crystal structure of flavin binding to fad synthetase from thermotoga maritina

Identifiers

Symbol

FAD_syn

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In molecular biology, the prokaryotic riboflavin biosynthesis protein is a bifunctional enzyme found in bacteria.

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase EC 2.7.1.26, which converts it into FMN, and FAD synthetase EC 2.7.7.2, which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme, the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family.^[1]^[2] The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases.^[3]

[edit] References

^ Karthikeyan S, Zhou Q, Osterman AL, Zhang H (November 2003). "Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism". Biochemistry 42 (43): 12532–8. doi:10.1021/bi035450t. PMID 14580199.
^ Galluccio M, Brizio C, Torchetti EM, Ferranti P, Gianazza E, Indiveri C, Barile M (March 2007). "Over-expression in Escherichia coli, purification and characterization of isoform 2 of human FAD synthetase". Protein Expr. Purif. 52 (1): 175–81. doi:10.1016/j.pep.2006.09.002. PMID 17049878.
^ Krupa A, Sandhya K, Srinivasan N, Jonnalagadda S (January 2003). "A conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer". Trends Biochem. Sci. 28 (1): 9–12. doi:10.1016/S0968-0004(02)00009-9. PMID 12517446.

This article incorporates text from the public domain Pfam and InterPro IPR015864

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.

FAD synthetase

This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity [1]. They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD [1]. This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity [2].

Literature references

Manstein DJ, Pai EF; , J Biol Chem 1986;261:16169-16173.: Purification and characterization of FAD synthetase from Brevibacterium ammoniagenes. PUBMED:3023344
Wang W, Kim R, Yokota H, Kim SH; , Proteins 2005;58:246-248.: Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. PUBMED:15468322

Clan

This family is a member of clan HUP (CL0039), which has a total of 26 members.

External database links

PANDIT:	PF06574
Pseudofam:	PF06574
SCOP:	1n05
SYSTERS:	FAD_syn

This tab holds annotation information from the InterPro database.

InterPro entry IPR015864

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (EC), which converts it into FMN, and FAD synthetase (EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [PUBMED:14580199], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family [PUBMED:17049878]. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases [PUBMED:12517446].

This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	FMN adenylyltransferase activity (GO:0003919)
Biological process	riboflavin biosynthetic process (GO:0009231)

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 HUP (CL0039), which contains the following 26 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 ATP_bind_4 Citrate_ly_lig CTP_transf_2 DNA_photolyase ETF ExsB FAD_syn HIGH_NTase1 NAD_synthase Pantoate_ligase PAPS_reduct 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 Usp

Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

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Alignment:	Seed (64) Full (3059) NCBI (2461) Metagenomics (2387)
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Alignment:	Seed (64) Full (3059)
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Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (64) Full (3059) NCBI (2461) Metagenomics (2387)
Full length sequences	Full-sequences (3059)

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.

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Trees

This page displays the phylogenetic tree for this family. 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 or full alignments.

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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_18632 (release 10.0)

Previous IDs:

Flavokinase;

Type:

Family

Author:

Moxon SJ, Mistry J, Eddy S

Number in seed:

64

Number in full:

3059

Average length of the domain:

151.70 aa

Average identity of full alignment:

31 %

Average coverage of the sequence by the domain:

48.43 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.6	20.6
Trusted cut-off	20.6	20.6
Noise cut-off	20.5	20.5

Model length:

158

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

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Archea	Eukaryota
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Viroids	Unclassified sequence

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 if you need to select sub-trees and view sequence alignments. More...

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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, it's distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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Interactions

There is 1 interaction for this family. More...

Flavokinase

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 FAD_syn domain has been found. There are 13 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.

Loading structure mapping...

Family: FAD_syn (PF06574)

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Summary: FAD synthetase

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Prokaryotic riboflavin biosynthesis protein

[edit] References

FAD synthetase

Literature references

Clan

External database links

InterPro entry IPR015864

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Viewing

Downloading

View options

Formatting options

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures