Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Elp3 Elongator protein 3, MiaB family, Radical SAM

SMART accession number:	SM00729
Description:	This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Interpro abstract (IPR006638):	This domain is found in MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases [ (PUBMED:11222759) ].
GO function:	catalytic activity (GO:0003824), iron-sulfur cluster binding (GO:0051536)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 276946 Elp3 domains in 276201 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Elp3 domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Elp3 domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Elp3 domain in the selected taxonomic class.

• Cellular role (predicted cellular role)

• Cellular role: chromatin
  Binding / catalysis: Methyltransferase

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Lash TD, Kaprak TA, Shen L, Jones MA
  • Metabolism of analogues of coproporphyrinogen-III with modified side chains: implications for binding at the active site of coproporphyrinogen oxidase.
  • Bioorg Med Chem Lett. 2002; 12: 451-6
  • Display abstract

  • Porphyrinogens with modified propionate side chains bearing methyl substituents were found to be modest substrates for coproporphyrinogen oxidase; the results indicate that alteration of the substituents involved in secondary binding interactions has a comparable affect to modifying the side chain that undergoes degradation at the catalytic site.

  • Wittschieben BO et al.
  • A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme.
  • Mol Cell. 1999; 4: 123-8
  • Display abstract

  • The elongator complex is a major component of the RNA polymerase II (RNAPII) holoenzyme responsible for transcriptional elongation in yeast. Here we identify Elp3, the 60-kilodalton subunit of elongator/RNAPII holoenzyme, as a highly conserved histone acetyltransferase (HAT) capable of acetylating core histones in vitro. In vivo, ELP3 gene deletion confers typical elp phenotypes such as slow growth adaptation, slow gene activation, and temperature sensitivity. These results suggest a role for a novel, tightly RNAPII-associated HAT in transcription of DNA packaged in chromatin.

  • Hidaka T, Hidaka M, Kuzuyama T, Seto H
  • Sequence of a P-methyltransferase-encoding gene isolated from a bialaphos-producing Streptomyces hygroscopicus.
  • Gene. 1995; 158: 149-50
  • Display abstract

  • The nucleotide sequence of the Streptomyces hygroscopicus gene encoding P-methyltransferase, catalyzing the formation of a carbon-phosphorus bond, involved in bialaphos biosynthesis, has been determined. The amino-acid sequence deduced from the nt sequence, shows homology with those of magnesium-protoporphyrin IX monomethyl ester oxidative cyclase (Mg-ProtoMe cyclase) of Rhodobacter capsulatus and the enzyme catalyzing the methylation of the aldehyde carbon of phosphonoacetaldehyde in fosfomycin biosynthesis.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 33.26 map00860 Porphyrin and chlorophyll metabolism 19.10 map00780 Biotin metabolism 17.45 map00785 Lipoic acid metabolism 14.32 map00790 Folate biosynthesis 2.52 map00310 Lysine degradation 2.21 map00730 Thiamine metabolism 2.10 map00910 Nitrogen metabolism 2.00 map00510 N-Glycan biosynthesis 0.77 map00380 Tryptophan metabolism 0.62 map00350 Tyrosine metabolism 0.62 map00340 Histidine metabolism 0.62 map00440 Aminophosphonate metabolism 0.62 map00626 Naphthalene and anthracene degradation 0.62 map00150 Androgen and estrogen metabolism 0.62 map00450 Selenoamino acid metabolism 0.41 map00351 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation 0.36 map00625 Tetrachloroethene degradation 0.31 map00363 Bisphenol A degradation 0.26 map00627 1,4-Dichlorobenzene degradation 0.15 map00628 Fluorene degradation 0.15 map00640 Propanoate metabolism 0.15 map00364 Fluorobenzoate degradation 0.10 map00120 Bile acid biosynthesis 0.10 map00624 1- and 2-Methylnaphthalene degradation 0.05 map00260 Glycine, serine and threonine metabolism 0.05 map00281 Geraniol degradation 0.05 map00650 Butanoate metabolism 0.05 map02020 Two-component system - General 0.05 map03060 Protein export 0.05 map00051 Fructose and mannose metabolism 0.05 map00280 Valine, leucine and isoleucine degradation 0.05 map02030 Bacterial chemotaxis - General 0.05 map00591 Linoleic acid metabolism 0.05 map00052 Galactose metabolism 0.05 map00230 Purine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with Elp3 domain which could be assigned to a KEGG orthologous group, and not all proteins containing Elp3 domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of Elp3 domains in PDB

  PDB code	Main view	Title
  1olt		Coproporphyrinogen III oxidase (HemN) from Escherichia coli is a Radical SAM enzyme.
  1r30		The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme
  1tv7		Structure of the S-adenosylmethionine dependent Enzyme MoaA
  1tv8		Structure of MoaA in complex with S-adenosylmethionine
  2fb2		Structure of the MoaA Arg17/266/268/Ala triple mutant
  2fb3		Structure of MoaA in complex with 5'-GTP
  2qgq		Crystal structure of TM_1862 from Thermotoga maritima. Northeast Structural Genomics Consortium target VR77
  2z2u		Crystal structure of archaeal TYW1
  3c8f		4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet
  3cb8		4Fe-4S-Pyruvate formate-lyase activating enzyme in complex with AdoMet and a peptide substrate
  3ciw		X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima
  3cix		X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate
  3iix		X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine
  3iiz		X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine
  3rf9		X-ray structure of RlmN from Escherichia coli
  3rfa		X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine
  3t7v		Crystal structure of methylornithine synthase (PylB)
  4jc0		Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77
  4jxc		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
  4jy8		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
  4jy9		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
  4jyd		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.
  4jye		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.
  4jyf		X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.
  4k36		His6 tagged anSMEcpe with bound AdoMet
  4k37		Native anSMEcpe with bound AdoMet
  4k38		Native anSMEcpe with bound AdoMet and Kp18Cys peptide
  4k39		Native anSMEcpe with bound AdoMet and Cp18Cys peptide
  4pl1		4PL1
  4pl2		4PL2
  4rtb		4RTB
  4u0o		4U0O
  4u0p		4U0P
  4wcx		4WCX
  5exi		5EXI
  5exj		5EXJ
  5exk		5EXK
  5fep		5FEP
  5fes		5FES
  5few		5FEW
  5fex		5FEX
  5fez		5FEZ
  5ff0		5FF0
  5ff2		5FF2
  5ff3		5FF3
  5ff4		5FF4
  5hr6		5HR6
  5hr7		5HR7
  5l7j		5L7J
  5l7l		5L7L

• Links (links to other resources describing this domain)

• PFAM	Radical_SAM
  INTERPRO	IPR006638

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