DPHB_ARCFU
ID DPHB_ARCFU Reviewed; 251 AA.
AC O29866;
DT 10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Diphthine synthase {ECO:0000255|HAMAP-Rule:MF_01084};
DE EC=2.1.1.98 {ECO:0000255|HAMAP-Rule:MF_01084};
DE AltName: Full=Diphthamide biosynthesis methyltransferase {ECO:0000255|HAMAP-Rule:MF_01084};
GN Name=dphB {ECO:0000255|HAMAP-Rule:MF_01084}; OrderedLocusNames=AF_0381;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 2-251.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
CC catalyzes the trimethylation of the amino group of the modified target
CC histidine residue in translation elongation factor 2 (EF-2), to form an
CC intermediate called diphthine. The three successive methylation
CC reactions represent the second step of diphthamide biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01084}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-[(3S)-amino-3-carboxypropyl]-L-histidyl-[translation
CC elongation factor 2] + 3 S-adenosyl-L-methionine = diphthine-
CC [translation elongation factor 2] + 3 H(+) + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:36415, Rhea:RHEA-COMP:9749, Rhea:RHEA-
CC COMP:10172, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73995, ChEBI:CHEBI:82696; EC=2.1.1.98;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01084};
CC -!- PATHWAY: Protein modification; peptidyl-diphthamide biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01084}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01084}.
CC -!- SIMILARITY: Belongs to the diphthine synthase family.
CC {ECO:0000255|HAMAP-Rule:MF_01084}.
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DR EMBL; AE000782; AAB90855.1; -; Genomic_DNA.
DR PIR; E69297; E69297.
DR RefSeq; WP_010877888.1; NC_000917.1.
DR PDB; 1VHV; X-ray; 1.75 A; A/B=2-251.
DR PDBsum; 1VHV; -.
DR AlphaFoldDB; O29866; -.
DR SMR; O29866; -.
DR STRING; 224325.AF_0381; -.
DR EnsemblBacteria; AAB90855; AAB90855; AF_0381.
DR GeneID; 24793920; -.
DR KEGG; afu:AF_0381; -.
DR eggNOG; arCOG04161; Archaea.
DR HOGENOM; CLU_066040_0_0_2; -.
DR OMA; TAGDPMV; -.
DR OrthoDB; 102360at2157; -.
DR PhylomeDB; O29866; -.
DR UniPathway; UPA00559; -.
DR EvolutionaryTrace; O29866; -.
DR Proteomes; UP000002199; Chromosome.
DR GO; GO:0004164; F:diphthine synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0017183; P:peptidyl-diphthamide biosynthetic process from peptidyl-histidine; IEA:UniProtKB-UniRule.
DR CDD; cd11647; DHP5_DphB; 1.
DR Gene3D; 3.30.950.10; -; 1.
DR Gene3D; 3.40.1010.10; -; 1.
DR HAMAP; MF_01084; Diphthine_synth; 1.
DR InterPro; IPR000878; 4pyrrol_Mease.
DR InterPro; IPR035996; 4pyrrol_Methylase_sf.
DR InterPro; IPR014777; 4pyrrole_Mease_sub1.
DR InterPro; IPR014776; 4pyrrole_Mease_sub2.
DR InterPro; IPR004551; Dphthn_synthase.
DR PANTHER; PTHR10882; PTHR10882; 1.
DR Pfam; PF00590; TP_methylase; 1.
DR PIRSF; PIRSF036432; Diphthine_synth; 1.
DR SUPFAM; SSF53790; SSF53790; 1.
DR TIGRFAMs; TIGR00522; dph5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..251
FT /note="Diphthine synthase"
FT /id="PRO_0000156115"
FT BINDING 9
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 84
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 87
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 112..113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 160
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 194
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT BINDING 219
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 8..11
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 17..25
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 42..49
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:1VHV"
FT TURN 62..64
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 65..72
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 75..83
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 90..100
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 105..108
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 113..121
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 155..160
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 181..185
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 186..193
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 206..211
FT /evidence="ECO:0007829|PDB:1VHV"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 230..239
FT /evidence="ECO:0007829|PDB:1VHV"
FT HELIX 244..249
FT /evidence="ECO:0007829|PDB:1VHV"
SQ SEQUENCE 251 AA; 28008 MW; 3C2D38D9C405B848 CRC64;
MLTFVGLGLW DVKDISVKGL EAVREADEVY VEYYTSKLLS SIEEMEEFFG KRVVELERSD
LEENSFRLIE RAKSKSVVLL VPGDPMVATT HSAIKLEAER KGVKTRIIHG ASISTAVCGL
TGLHNYRFGK SATVSWHRSQ TPVNVIKANR SIDAHTLLFL DLHPEPMTIG HAVENLIAED
AQMKDLYAVG IARAGSGEEV VKCDRLENLK KIDFGKPLHV MVVLAKTLHF MEFECLREFA
DAPAELERLV A
