DPHB_AERPE
ID DPHB_AERPE Reviewed; 294 AA.
AC Q9YDI2;
DT 10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Diphthine synthase;
DE EC=2.1.1.98;
DE AltName: Full=Diphthamide biosynthesis methyltransferase;
GN Name=dphB; OrderedLocusNames=APE_0931;
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=18391406; DOI=10.1107/s0907444908000723;
RA Kishishita S., Shimizu K., Murayama K., Terada T., Shirouzu M.,
RA Yokoyama S., Kunishima N.;
RT "Structures of two archaeal diphthine synthases: insights into the post-
RT translational modification of elongation factor 2.";
RL Acta Crystallogr. D 64:397-406(2008).
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 (By
CC similarity). {ECO:0000250}.
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 -!- PATHWAY: Protein modification; peptidyl-diphthamide biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the diphthine synthase family. {ECO:0000305}.
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DR EMBL; BA000002; BAA79915.1; -; Genomic_DNA.
DR PIR; C72689; C72689.
DR PDB; 1WDE; X-ray; 2.00 A; A=1-294.
DR PDBsum; 1WDE; -.
DR AlphaFoldDB; Q9YDI2; -.
DR SMR; Q9YDI2; -.
DR STRING; 272557.APE_0931; -.
DR EnsemblBacteria; BAA79915; BAA79915; APE_0931.
DR KEGG; ape:APE_0931; -.
DR PATRIC; fig|272557.25.peg.669; -.
DR eggNOG; arCOG04161; Archaea.
DR OMA; TAGDPMV; -.
DR BRENDA; 2.1.1.98; 171.
DR UniPathway; UPA00559; -.
DR EvolutionaryTrace; Q9YDI2; -.
DR Proteomes; UP000002518; 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..294
FT /note="Diphthine synthase"
FT /id="PRO_0000156114"
FT BINDING 93
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 96
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 121..122
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 173
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 220
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT STRAND 9..14
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 24..32
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 48..57
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 67..71
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 85..92
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 100..109
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 122..130
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 153..164
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 168..173
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 184..202
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 208..210
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 213..217
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 225..230
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 232..236
FT /evidence="ECO:0007829|PDB:1WDE"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 255..264
FT /evidence="ECO:0007829|PDB:1WDE"
FT HELIX 277..287
FT /evidence="ECO:0007829|PDB:1WDE"
FT TURN 288..290
FT /evidence="ECO:0007829|PDB:1WDE"
SQ SEQUENCE 294 AA; 31451 MW; 521C3A3C2B206C90 CRC64;
MARGREAVTL LLVGWGYAPG MQTLEALDAV RRADVVYVES YTMPGSSWLY KSVVEAAGEA
RVVEASRRDL EERSREIVSR ALDAVVAVVT AGDPMVATTH SSLAAEALEA GVAVRYIPGV
SGVQAARGAT MLSFYRFGGT VTLPGPWRGV TPISVARRIY LNLCAGLHTT ALLDVDERGV
QLSPGQGVSL LLEADREYAR EAGAPALLAR LPSVLVEAGA GGGHRVLYWS SLERLSTADV
EGGVYSIVIP ARLSGVEEWL LAAASGQRRP LEYDRSVYET VEENCKKGVY MEPV
