DPHB_PYRHO
ID DPHB_PYRHO Reviewed; 265 AA.
AC O58456;
DT 10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Diphthine synthase {ECO:0000255|HAMAP-Rule:MF_01084, ECO:0000303|PubMed:18391406};
DE EC=2.1.1.98 {ECO:0000255|HAMAP-Rule:MF_01084, ECO:0000269|PubMed:20873788};
DE AltName: Full=Diphthamide biosynthesis methyltransferase {ECO:0000255|HAMAP-Rule:MF_01084};
GN Name=dphB {ECO:0000255|HAMAP-Rule:MF_01084};
GN Synonyms=dph5 {ECO:0000303|PubMed:20873788}; OrderedLocusNames=PH0725;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=20873788; DOI=10.1021/bi100812h;
RA Zhu X., Kim J., Su X., Lin H.;
RT "Reconstitution of diphthine synthase activity in vitro.";
RL Biochemistry 49:9649-9657(2010).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
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).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3.";
RL Submitted (FEB-2009) to the PDB data bank.
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, ECO:0000269|PubMed:20873788}.
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 ECO:0000269|PubMed:20873788};
CC -!- PATHWAY: Protein modification; peptidyl-diphthamide biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01084, ECO:0000269|PubMed:20873788}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01084,
CC ECO:0000269|PubMed:18391406, ECO:0000269|Ref.4}.
CC -!- MISCELLANEOUS: The diphthine intermediate is not stable in vitro and
CC readily eliminates the trimethylamino group. It is not known whether
CC the elimination reaction also occurs physiologically.
CC -!- SIMILARITY: Belongs to the diphthine synthase family.
CC {ECO:0000255|HAMAP-Rule:MF_01084, ECO:0000305}.
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DR EMBL; BA000001; BAA29816.1; -; Genomic_DNA.
DR PIR; F71119; F71119.
DR RefSeq; WP_010884823.1; NC_000961.1.
DR PDB; 1VCE; X-ray; 2.10 A; A/B=1-265.
DR PDB; 1WNG; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2DEK; X-ray; 1.65 A; A/B=1-265.
DR PDB; 2DSG; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2DSH; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2DSI; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2DV3; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2DV4; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2DV5; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2DV7; X-ray; 2.30 A; A/B=1-265.
DR PDB; 2DXV; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2DXW; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2DXX; X-ray; 1.75 A; A/B=1-265.
DR PDB; 2E07; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2E08; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2E15; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2E16; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2E17; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2E4N; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2E4R; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2E7R; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2E8H; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2E8Q; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2E8R; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2E8S; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2ED3; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2ED5; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2EEQ; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2EGB; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2EGL; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2EGS; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2EH2; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2EH4; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2EH5; X-ray; 2.30 A; A/B=1-265.
DR PDB; 2EHC; X-ray; 1.80 A; A/B=1-265.
DR PDB; 2EHL; X-ray; 1.60 A; A/B=1-265.
DR PDB; 2EJJ; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2EJK; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2EJZ; X-ray; 1.85 A; A/B=1-265.
DR PDB; 2EK2; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2EK3; X-ray; 2.80 A; A/B=1-265.
DR PDB; 2EK4; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2EK7; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2EKA; X-ray; 2.30 A; A/B=1-265.
DR PDB; 2EL0; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2EL1; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2EL2; X-ray; 2.30 A; A/B=1-265.
DR PDB; 2EL3; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2ELD; X-ray; 2.30 A; A/B=1-265.
DR PDB; 2ELE; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2EMR; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2EMU; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2EN5; X-ray; 1.90 A; A/B=1-265.
DR PDB; 2ENI; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2HR8; X-ray; 2.80 A; A/B=1-265.
DR PDB; 2HUQ; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2HUT; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2HUV; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2HUX; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2OWF; X-ray; 2.20 A; A=1-265.
DR PDB; 2OWG; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2OWK; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2OWU; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2OWV; X-ray; 2.80 A; A/B=1-265.
DR PDB; 2P2X; X-ray; 2.90 A; A/B=1-265.
DR PDB; 2P5C; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2P5F; X-ray; 2.50 A; A/B=1-265.
DR PDB; 2P6D; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2P6I; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2P6K; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2P6L; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2P9D; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2PB4; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2PB5; X-ray; 2.10 A; A/B=1-265.
DR PDB; 2PB6; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2PCA; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2PCG; X-ray; 2.20 A; A/B=1-265.
DR PDB; 2PCH; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2PCI; X-ray; 2.00 A; A/B=1-265.
DR PDB; 2PCK; X-ray; 2.60 A; A/B=1-265.
DR PDB; 2PCM; X-ray; 2.40 A; A/B=1-265.
DR PDB; 2Z6R; X-ray; 1.50 A; A/B=1-265.
DR PDBsum; 1VCE; -.
DR PDBsum; 1WNG; -.
DR PDBsum; 2DEK; -.
DR PDBsum; 2DSG; -.
DR PDBsum; 2DSH; -.
DR PDBsum; 2DSI; -.
DR PDBsum; 2DV3; -.
DR PDBsum; 2DV4; -.
DR PDBsum; 2DV5; -.
DR PDBsum; 2DV7; -.
DR PDBsum; 2DXV; -.
DR PDBsum; 2DXW; -.
DR PDBsum; 2DXX; -.
DR PDBsum; 2E07; -.
DR PDBsum; 2E08; -.
DR PDBsum; 2E15; -.
DR PDBsum; 2E16; -.
DR PDBsum; 2E17; -.
DR PDBsum; 2E4N; -.
DR PDBsum; 2E4R; -.
DR PDBsum; 2E7R; -.
DR PDBsum; 2E8H; -.
DR PDBsum; 2E8Q; -.
DR PDBsum; 2E8R; -.
DR PDBsum; 2E8S; -.
DR PDBsum; 2ED3; -.
DR PDBsum; 2ED5; -.
DR PDBsum; 2EEQ; -.
DR PDBsum; 2EGB; -.
DR PDBsum; 2EGL; -.
DR PDBsum; 2EGS; -.
DR PDBsum; 2EH2; -.
DR PDBsum; 2EH4; -.
DR PDBsum; 2EH5; -.
DR PDBsum; 2EHC; -.
DR PDBsum; 2EHL; -.
DR PDBsum; 2EJJ; -.
DR PDBsum; 2EJK; -.
DR PDBsum; 2EJZ; -.
DR PDBsum; 2EK2; -.
DR PDBsum; 2EK3; -.
DR PDBsum; 2EK4; -.
DR PDBsum; 2EK7; -.
DR PDBsum; 2EKA; -.
DR PDBsum; 2EL0; -.
DR PDBsum; 2EL1; -.
DR PDBsum; 2EL2; -.
DR PDBsum; 2EL3; -.
DR PDBsum; 2ELD; -.
DR PDBsum; 2ELE; -.
DR PDBsum; 2EMR; -.
DR PDBsum; 2EMU; -.
DR PDBsum; 2EN5; -.
DR PDBsum; 2ENI; -.
DR PDBsum; 2HR8; -.
DR PDBsum; 2HUQ; -.
DR PDBsum; 2HUT; -.
DR PDBsum; 2HUV; -.
DR PDBsum; 2HUX; -.
DR PDBsum; 2OWF; -.
DR PDBsum; 2OWG; -.
DR PDBsum; 2OWK; -.
DR PDBsum; 2OWU; -.
DR PDBsum; 2OWV; -.
DR PDBsum; 2P2X; -.
DR PDBsum; 2P5C; -.
DR PDBsum; 2P5F; -.
DR PDBsum; 2P6D; -.
DR PDBsum; 2P6I; -.
DR PDBsum; 2P6K; -.
DR PDBsum; 2P6L; -.
DR PDBsum; 2P9D; -.
DR PDBsum; 2PB4; -.
DR PDBsum; 2PB5; -.
DR PDBsum; 2PB6; -.
DR PDBsum; 2PCA; -.
DR PDBsum; 2PCG; -.
DR PDBsum; 2PCH; -.
DR PDBsum; 2PCI; -.
DR PDBsum; 2PCK; -.
DR PDBsum; 2PCM; -.
DR PDBsum; 2Z6R; -.
DR AlphaFoldDB; O58456; -.
DR SMR; O58456; -.
DR STRING; 70601.3257133; -.
DR PRIDE; O58456; -.
DR EnsemblBacteria; BAA29816; BAA29816; BAA29816.
DR GeneID; 1443058; -.
DR KEGG; pho:PH0725; -.
DR eggNOG; arCOG04161; Archaea.
DR OMA; TAGDPMV; -.
DR OrthoDB; 102360at2157; -.
DR BioCyc; MetaCyc:MON-18825; -.
DR BRENDA; 2.1.1.98; 5244.
DR UniPathway; UPA00559; -.
DR EvolutionaryTrace; O58456; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0004164; F:diphthine synthase activity; IDA:UniProtKB.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0017183; P:peptidyl-diphthamide biosynthetic process from peptidyl-histidine; IDA:UniProtKB.
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; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..265
FT /note="Diphthine synthase"
FT /id="PRO_0000156126"
FT BINDING 10
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 87
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 90
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 115..116
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 166
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 209
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT BINDING 234
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01084,
FT ECO:0000305|PubMed:18391406, ECO:0000305|Ref.4"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 18..26
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:2E7R"
FT HELIX 44..51
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 60..70
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 80..86
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 95..103
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:2OWF"
FT HELIX 147..157
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 178..192
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 202..208
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 221..224
FT /evidence="ECO:0007829|PDB:2Z6R"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 244..254
FT /evidence="ECO:0007829|PDB:2Z6R"
FT HELIX 258..261
FT /evidence="ECO:0007829|PDB:2Z6R"
SQ SEQUENCE 265 AA; 29576 MW; E0F313144BEECC91 CRC64;
MVLYFIGLGL YDERDITVKG LEIAKKCDYV FAEFYTSLMA GTTLGRIQKL IGKEIRVLSR
EDVELNFENI VLPLAKENDV AFLTPGDPLV ATTHAELRIR AKRAGVESYV IHAPSIYSAV
GITGLHIYKF GKSATVAYPE GNWFPTSYYD VIKENAERGL HTLLFLDIKA EKRMYMTANE
AMELLLKVED MKKGGVFTDD TLVVVLARAG SLNPTIRAGY VKDLIREDFG DPPHILIVPG
KLHIVEAEYL VEIAGAPREI LRVNV
