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47  structures 6523  species 4  interactions 7948  sequences 68  architectures

Family: YjeF_N (PF03853)

Summary: YjeF-related protein N-terminus

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This is the Wikipedia entry entitled "YjeF N terminal protein domain". More...

YjeF N terminal protein domain Edit Wikipedia article

PDB 1jzt EBI.jpg
crystal structure of yeast ynu0, ynl200c
Symbol YjeF_N
Pfam PF03853
InterPro IPR004443
SCOP 1jzt

In molecular biology, the YjeF N terminal is a protein domain found in the N-terminal of the protein, EDC3. The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes. They help assemble the processing body (P-body) in preparation for mRNAdecay. Structural homology indicated it may have some similarity to the enzyme family, hydrolase.


At the cellular level, the YjeF-N terminal domain is vital to the assembly of the processing body (P-body). This aids mRNA decay and is thought to bring together different complexes to aggregate mRNPs.[1] At the organism level, in bacteria and archaea, YjeF N-terminal domains are often fused to a YjeF C-terminal domain with high structural homology to the members of a ribokinase-like superfamily or belong to operons that encode enzymes of diverse functions. Examples of such include:

  • pyridoxal phosphate biosynthetic protein PdxJ;
  • phosphopanteine-protein transferase;
  • ATP/GTP hydrolase;
  • and pyruvate-formate lyase 1-activating enzyme.

In plants, the YjeF N-terminal domain is fused to a C-terminal putative pyridoxamine 5'-phosphate oxidase. In eukaryotes, proteins that consist of (Sm)-FDF-YjeF N-terminal domains may be involved in RNA processing.[2][3]


The YjeF N-terminal domains represent a novel version of the Rossmann fold, one of the most common protein folds in nature. The YjeF N-terminal domain is a three-layer alpha-beta-alpha sandwich with a central beta-sheet surrounded by alpha helices. The conservation of the acidic residues in the predicted active site of the YjeF N-terminal domains shows some similarities to the amino acids found in the active sites of diverse hydrolases.[2][3]


  1. ^ Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H (2008). "Crystal structure of human Edc3 and its functional implications.". Mol Cell Biol. 28 (19): 5965–76. doi:10.1128/MCB.00761-08. PMC 2547010Freely accessible. PMID 18678652. 
  2. ^ a b Anantharaman V, Aravind L (July 2004). "Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability". BMC Genomics. 5 (1): 45. doi:10.1186/1471-2164-5-45. PMC 503384Freely accessible. PMID 15257761. 
  3. ^ a b Jha KN, Shumilin IA, Digilio LC, Chertihin O, Zheng H, Schmitz G, Visconti PE, Flickinger CJ, Minor W, Herr JC (May 2008). "Biochemical and structural characterization of apolipoprotein A-I binding protein, a novel phosphoprotein with a potential role in sperm capacitation". Endocrinology. 149 (5): 2108–20. doi:10.1210/en.2007-0582. PMC 2329272Freely accessible. PMID 18202122. 

This article incorporates text from the public domain Pfam and InterPro IPR004443

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.

YjeF-related protein N-terminus Provide feedback

YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1] where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1].

Literature references

  1. Anantharaman V, Aravind L;, BMC Genomics. 2004;5:45.: Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. PUBMED:15257761 EPMC:15257761

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004443

In bacteria or archaea, YjeF N-terminal domains occur either as single proteins or fused with other domains and are commonly associated with enzymes. YjeF N-terminal domains are often fused to a YjeF C-terminal domain. It is a bifunctional enzyme that catalyses the epimerisation of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP [PUBMED:21994945].

Structurally, YjeF N-terminal domains represent a novel version of the Rossmann fold, one of the most common protein folds in nature. The YjeF N-terminal domain is comprised of a three-layer alpha-beta-alpha sandwich with a central beta-sheet surrounded by helices. This domain contains a putative catalytic site [PUBMED:15257761].

The YjeF N-terminal domain is homologous to AIBP in mammals and YNL200C in budding yeasts. AIBP and YNL200C are NAD(P)H-hydrate epimerases that catalyses the epimerisation of the S- and R-forms of NAD(P)HX, at the expense of ATP, which is converted to ADP [PUBMED:21994945].

Some proteins known to contain a YjeF N-terminal domain are listed below:

  • Escherichia coli hypothetical protein YjeF.
  • Thermotoga maritima hypothetical protein Tm0922.
  • Yeast uncharacterised protein YNL200C.
  • Yeast enhancer of mRNA-decapping protein 3 (EDC3).
  • Vertebrate enhancer of mRNA-decapping protein 3 (EDC3).
  • Mammalian apolipoprotein A-I binding protein (AI-BP).

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 NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 204 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_Methyltr_1 CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1188 DUF1442 DUF1611_N DUF166 DUF1776 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 DUF5129 DUF5130 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecB GMC_oxred_N Gp_dh_N GRAS GRDA HI0933_like HIM1 IlvN ISPD_C K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall Orbi_VP4 PALP PARP_regulatory PCMT PDH PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N


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Curation and family details

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Curation View help on the curation process

Seed source: TIGRFAMs
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: TIGRFAMs, Griffiths-Jones SR
Number in seed: 52
Number in full: 7948
Average length of the domain: 166.00 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 35.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.9 24.9
Trusted cut-off 25.0 25.0
Noise cut-off 24.8 24.8
Model length: 171
Family (HMM) version: 16
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Species distribution

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Colour assignments

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


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There are 4 interactions for this family. More...

FDF FDF Carb_kinase YjeF_N


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 YjeF_N domain has been found. There are 47 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.

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