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17  structures 4320  species 1  interaction 4652  sequences 15  architectures

Family: FAD_syn (PF06574)

Summary: FAD synthetase

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This is the Wikipedia entry entitled "Prokaryotic riboflavin biosynthesis protein". More...

Prokaryotic riboflavin biosynthesis protein Edit Wikipedia article

FAD synthetase
PDB 1s4m EBI.jpg
crystal structure of flavin binding to fad synthetase from thermotoga maritina
Identifiers
Symbol FAD_syn
Pfam PF06574
Pfam clan CL0119
InterPro IPR015864
SCOP 1n05
SUPERFAMILY 1n05

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]

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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 Provide feedback

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

  1. Manstein DJ, Pai EF; , J Biol Chem 1986;261:16169-16173.: Purification and characterization of FAD synthetase from Brevibacterium ammoniagenes. PUBMED:3023344 EPMC:3023344

  2. 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 EPMC:15468322


External database links

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

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Domain organisation

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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 26 members:

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

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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
(62)
Full
(4652)
Representative proteomes NCBI
(3311)
Meta
(2386)
RP15
(342)
RP35
(672)
RP55
(856)
RP75
(995)
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Format an alignment

  Seed
(62)
Full
(4652)
Representative proteomes NCBI
(3311)
Meta
(2386)
RP15
(342)
RP35
(672)
RP55
(856)
RP75
(995)
Alignment:
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Sequence:
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  Seed
(62)
Full
(4652)
Representative proteomes NCBI
(3311)
Meta
(2386)
RP15
(342)
RP35
(672)
RP55
(856)
RP75
(995)
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.

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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

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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 View help on the curation process

Seed source: Pfam-B_18632 (release 10.0)
Previous IDs: Flavokinase;
Type: Family
Author: Moxon SJ, Mistry J, Eddy S
Number in seed: 62
Number in full: 4652
Average length of the domain: 148.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 49.28 %

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 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
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Species distribution

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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 17 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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