DPH3_SCHPO
ID DPH3_SCHPO Reviewed; 79 AA.
AC Q9UT33;
DT 04-APR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Diphthamide biosynthesis protein 3;
GN Name=dph3; ORFNames=SPAC8F11.02c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP DISRUPTION PHENOTYPE.
RX PubMed=28555368; DOI=10.1007/s00294-017-0711-x;
RA Villahermosa D., Knapp K., Fleck O.;
RT "A mutated dph3 gene causes sensitivity of Schizosaccharomyces pombe cells
RT to cytotoxic agents.";
RL Curr. Genet. 63:1081-1091(2017).
RN [3]
RP DISRUPTION PHENOTYPE.
RX PubMed=28775286; DOI=10.1038/s41598-017-07647-1;
RA Villahermosa D., Fleck O.;
RT "Elp3 and Dph3 of Schizosaccharomyces pombe mediate cellular stress
RT responses through tRNALysUUU modifications.";
RL Sci. Rep. 7:7225-7225(2017).
CC -!- FUNCTION: Required for the first step of diphthamide biosynthesis, a
CC post-translational modification of histidine which occurs in elongation
CC factor 2. Dph1 and dph2 transfer a 3-amino-3-carboxypropyl (ACP) group
CC from S-adenosyl-L-methionine (SAM) to a histidine residue, the reaction
CC is assisted by a reduction system comprising dph3 and a NADH-dependent
CC reductase, predominantly cbr1. Acts as an electron donor to reduce the
CC Fe-S cluster in dph1-dph2 keeping the [4Fe-4S] clusters in the active
CC and reduced state. Restores iron to dph1-dph2 iron-sulfur clusters
CC which have degraded from [4Fe-4S] to [3Fe-4S] by donating an iron atom
CC to reform [4Fe-4S] clusters, in a manner dependent on the presence of
CC elongation factor 2 and SAM. Associates with the elongator complex and
CC is required for tRNA Wobble base modifications mediated by the
CC elongator complex. The elongator complex is required for multiple tRNA
CC modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s
CC 2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-
CC carbamoylmethyl uridine). {ECO:0000250|UniProtKB:Q3E840}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[3Fe-4S](1+)-[protein] + Fe(2+)-[Dph3] = [3Fe-4S](0)-[protein]
CC + Fe(3+)-[Dph3]; Xref=Rhea:RHEA:71235, Rhea:RHEA-COMP:17996,
CC Rhea:RHEA-COMP:17997, Rhea:RHEA-COMP:18002, Rhea:RHEA-COMP:18003,
CC ChEBI:CHEBI:29033, ChEBI:CHEBI:29034, ChEBI:CHEBI:33751,
CC ChEBI:CHEBI:47402, ChEBI:CHEBI:83228;
CC Evidence={ECO:0000250|UniProtKB:Q3E840};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 [3Fe-4S](0)-[protein] + 2 Fe(2+)-[Dph3] + NADH = 2 [4Fe-
CC 4S](1+)-[protein] + 2 [Dph3] + H(+) + NAD(+); Xref=Rhea:RHEA:71239,
CC Rhea:RHEA-COMP:17997, Rhea:RHEA-COMP:17998, Rhea:RHEA-COMP:18001,
CC Rhea:RHEA-COMP:18002, ChEBI:CHEBI:15378, ChEBI:CHEBI:29033,
CC ChEBI:CHEBI:33723, ChEBI:CHEBI:47402, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:83228;
CC Evidence={ECO:0000250|UniProtKB:Q3E840};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q3E840};
CC -!- PATHWAY: Protein modification; peptidyl-diphthamide biosynthesis.
CC {ECO:0000250|UniProtKB:Q3E840}.
CC -!- SUBUNIT: Component of the 2-(3-amino-3-carboxypropyl)histidine synthase
CC complex composed of dph1, dph2, dph3 and a NADH-dependent reductase,
CC predominantly cbr1. {ECO:0000250|UniProtKB:Q3E840}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.
CC -!- DOMAIN: The DPH-type metal-binding (MB) domain can also bind zinc.
CC However, iron is the physiological binding partner as zinc binding
CC impairs the protein electron donor function.
CC {ECO:0000250|UniProtKB:Q3E840}.
CC -!- DISRUPTION PHENOTYPE: Sensitive to sordarin (fungicide), methyl
CC methanesulfonate (MMS, causes DNA breaks), hydroxyurea (HU,
CC ribonucleotide reductase inhibitor), thiabendazole (TBZ), sirolimus
CC (TORC1 inhibitor), thermal stress, and cold (PubMed:28555368,
CC PubMed:28775286). Simultaneous disruption of atf1 exacerbates
CC sensitivity to HU and MMS (PubMed:28775286). Global protein levels are
CC unaffected (PubMed:28775286). {ECO:0000269|PubMed:28555368,
CC ECO:0000269|PubMed:28775286}.
CC -!- SIMILARITY: Belongs to the DPH3 family. {ECO:0000305}.
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DR EMBL; CU329670; CAB52163.1; -; Genomic_DNA.
DR PIR; T39177; T39177.
DR RefSeq; NP_593951.1; NM_001019378.2.
DR AlphaFoldDB; Q9UT33; -.
DR SMR; Q9UT33; -.
DR BioGRID; 279854; 53.
DR STRING; 4896.SPAC8F11.02c.1; -.
DR PaxDb; Q9UT33; -.
DR EnsemblFungi; SPAC8F11.02c.1; SPAC8F11.02c.1:pep; SPAC8F11.02c.
DR PomBase; SPAC8F11.02c; dph3.
DR VEuPathDB; FungiDB:SPAC8F11.02c; -.
DR eggNOG; KOG2923; Eukaryota.
DR HOGENOM; CLU_155991_4_1_1; -.
DR InParanoid; Q9UT33; -.
DR OMA; LFTYPCP; -.
DR PhylomeDB; Q9UT33; -.
DR Reactome; R-SPO-5358493; Synthesis of diphthamide-EEF2.
DR UniPathway; UPA00559; -.
DR PRO; PR:Q9UT33; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0008198; F:ferrous iron binding; ISS:UniProtKB.
DR GO; GO:0034986; F:iron chaperone activity; ISS:UniProtKB.
DR GO; GO:0016491; F:oxidoreductase activity; ISS:UniProtKB.
DR GO; GO:0017183; P:peptidyl-diphthamide biosynthetic process from peptidyl-histidine; ISS:UniProtKB.
DR GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; ISS:UniProtKB.
DR GO; GO:0002098; P:tRNA wobble uridine modification; ISO:PomBase.
DR Gene3D; 3.10.660.10; -; 1.
DR InterPro; IPR044248; DPH3/4-like.
DR InterPro; IPR007872; DPH_MB_dom.
DR InterPro; IPR036671; DPH_MB_sf.
DR PANTHER; PTHR21454; PTHR21454; 1.
DR Pfam; PF05207; zf-CSL; 1.
DR SUPFAM; SSF144217; SSF144217; 1.
DR PROSITE; PS51074; DPH_MB; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..79
FT /note="Diphthamide biosynthesis protein 3"
FT /id="PRO_0000082636"
FT DOMAIN 3..59
FT /note="DPH-type MB"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00456"
FT BINDING 25
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q3E840"
FT BINDING 27
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q3E840"
FT BINDING 47
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q3E840"
FT BINDING 50
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q3E840"
SQ SEQUENCE 79 AA; 8897 MW; B3778B36947F7F5E CRC64;
MSFYDEIELE DFTFDAGTNL YTFPCPCGDR FEISLEDLQL GEDVARCPSC SLIVRVIYDE
DEFMEVDNDA STAPIIIAA
