HYDE_THEMA
ID HYDE_THEMA Reviewed; 348 AA.
AC Q9X0Z6; G4FE79;
DT 24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=[FeFe] hydrogenase maturase subunit HydE {ECO:0000305};
DE EC=1.8.-.- {ECO:0000305};
GN OrderedLocusNames=TM_1269 {ECO:0000312|EMBL:AAD36344.1};
GN ORFNames=THEMA_07990 {ECO:0000312|EMBL:AHD18826.1},
GN Tmari_1274 {ECO:0000312|EMBL:AGL50198.1};
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274 {ECO:0000312|EMBL:AAD36344.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2] {ECO:0000312|EMBL:AGL50198.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=23637642; DOI=10.1371/journal.pgen.1003485;
RA Latif H., Lerman J.A., Portnoy V.A., Tarasova Y., Nagarajan H.,
RA Schrimpe-Rutledge A.C., Smith R.D., Adkins J.N., Lee D.H., Qiu Y.,
RA Zengler K.;
RT "The genome organization of Thermotoga maritima reflects its lifestyle.";
RL PLoS Genet. 9:E1003485-E1003485(2013).
RN [3]
RP FUNCTION, SUBUNIT, COFACTOR, AND MUTAGENESIS OF CYS-63; CYS-67 AND CYS-70.
RX PubMed=16137685; DOI=10.1016/j.febslet.2005.07.092;
RA Rubach J.K., Brazzolotto X., Gaillard J., Fontecave M.;
RT "Biochemical characterization of the HydE and HydG iron-only hydrogenase
RT maturation enzymes from Thermatoga maritima.";
RL FEBS Lett. 579:5055-5060(2005).
RN [4] {ECO:0007744|PDB:3CIW, ECO:0007744|PDB:3CIX}
RP X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
RP (2FE-2S); IRON-SULFUR (4FE-4S-S-ADOMET), SUBUNIT, AND COFACTOR.
RX PubMed=18400755; DOI=10.1074/jbc.m801161200;
RA Nicolet Y., Rubach J.K., Posewitz M.C., Amara P., Mathevon C., Atta M.,
RA Fontecave M., Fontecilla-Camps J.C.;
RT "X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga
RT maritima.";
RL J. Biol. Chem. 283:18861-18872(2008).
RN [5] {ECO:0007744|PDB:3IIX, ECO:0007744|PDB:3IIZ}
RP X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (2FE-2S)
RP AND IRON-SULFUR (4FE-4S-S-ADOMET), AND COFACTOR.
RX PubMed=19706452; DOI=10.1073/pnas.0904385106;
RA Nicolet Y., Amara P., Mouesca J.M., Fontecilla-Camps J.C.;
RT "Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM
RT proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:14867-14871(2009).
RN [6] {ECO:0007744|PDB:4JXC, ECO:0007744|PDB:4JY8, ECO:0007744|PDB:4JY9}
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (2FE-2S)
RP AND IRON-SULFUR (4FE-4S-S-ADOMET), AND COFACTOR.
RX PubMed=23596207; DOI=10.1073/pnas.1302388110;
RA Nicolet Y., Rohac R., Martin L., Fontecilla-Camps J.C.;
RT "X-ray snapshots of possible intermediates in the time course of synthesis
RT and degradation of protein-bound Fe4S4 clusters.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:7188-7192(2013).
CC -!- FUNCTION: Required for the maturation of the [FeFe]-hydrogenase HydA
CC (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-
CC methionine (in vitro), suggesting it may contribute to the biosynthesis
CC of an essential sulfur-containing ligand that binds to the hydrogenase
CC active site [2Fe-2S] cluster (PubMed:16137685).
CC {ECO:0000250|UniProtKB:Q97IK9, ECO:0000269|PubMed:16137685,
CC ECO:0000305}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|PIRSR:PIRSR004762-1,
CC ECO:0000269|PubMed:16137685, ECO:0000269|PubMed:18400755,
CC ECO:0000269|PubMed:19706452, ECO:0000269|PubMed:23596207};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000255|PIRSR:PIRSR004762-1, ECO:0000269|PubMed:18400755,
CC ECO:0000269|PubMed:19706452, ECO:0000269|PubMed:23596207};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:18400755, ECO:0000269|PubMed:19706452,
CC ECO:0000269|PubMed:23596207};
CC Note=Binds 1 [2Fe-2S] cluster. {ECO:0000269|PubMed:18400755,
CC ECO:0000269|PubMed:19706452, ECO:0000269|PubMed:23596207};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16137685,
CC ECO:0000269|PubMed:18400755}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. HydE family.
CC {ECO:0000305}.
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DR EMBL; AE000512; AAD36344.1; -; Genomic_DNA.
DR EMBL; CP004077; AGL50198.1; -; Genomic_DNA.
DR EMBL; CP007013; AHD18826.1; -; Genomic_DNA.
DR PIR; D72274; D72274.
DR RefSeq; NP_229074.1; NC_000853.1.
DR RefSeq; WP_004079975.1; NZ_CP011107.1.
DR PDB; 3CIW; X-ray; 1.35 A; A=1-348.
DR PDB; 3CIX; X-ray; 1.70 A; A=1-348.
DR PDB; 3IIX; X-ray; 1.25 A; A=1-348.
DR PDB; 3IIZ; X-ray; 1.62 A; A=1-348.
DR PDB; 4JXC; X-ray; 1.50 A; A=1-348.
DR PDB; 4JY8; X-ray; 2.90 A; A=2-348.
DR PDB; 4JY9; X-ray; 1.60 A; A=1-348.
DR PDB; 4JYD; X-ray; 1.71 A; A=1-348.
DR PDB; 4JYE; X-ray; 1.65 A; A=1-348.
DR PDB; 4JYF; X-ray; 1.45 A; A=1-348.
DR PDB; 5FEP; X-ray; 1.45 A; A=2-348.
DR PDB; 5FES; X-ray; 1.27 A; A=2-348.
DR PDB; 5FEW; X-ray; 1.17 A; A=2-348.
DR PDB; 5FEX; X-ray; 1.32 A; A=2-348.
DR PDB; 5FEZ; X-ray; 1.35 A; A=2-348.
DR PDB; 5FF0; X-ray; 1.49 A; A=2-348.
DR PDB; 5FF2; X-ray; 1.47 A; A=1-348.
DR PDB; 5FF3; X-ray; 1.18 A; A=1-348.
DR PDB; 5FF4; X-ray; 1.35 A; A=2-348.
DR PDB; 7O1O; X-ray; 1.25 A; A=2-345.
DR PDB; 7O1P; X-ray; 2.58 A; A=2-348.
DR PDB; 7O1S; X-ray; 1.39 A; A=1-348.
DR PDB; 7O1T; X-ray; 1.50 A; A=2-348.
DR PDB; 7O25; X-ray; 1.34 A; A=2-348.
DR PDB; 7O26; X-ray; 1.50 A; A=1-348.
DR PDBsum; 3CIW; -.
DR PDBsum; 3CIX; -.
DR PDBsum; 3IIX; -.
DR PDBsum; 3IIZ; -.
DR PDBsum; 4JXC; -.
DR PDBsum; 4JY8; -.
DR PDBsum; 4JY9; -.
DR PDBsum; 4JYD; -.
DR PDBsum; 4JYE; -.
DR PDBsum; 4JYF; -.
DR PDBsum; 5FEP; -.
DR PDBsum; 5FES; -.
DR PDBsum; 5FEW; -.
DR PDBsum; 5FEX; -.
DR PDBsum; 5FEZ; -.
DR PDBsum; 5FF0; -.
DR PDBsum; 5FF2; -.
DR PDBsum; 5FF3; -.
DR PDBsum; 5FF4; -.
DR PDBsum; 7O1O; -.
DR PDBsum; 7O1P; -.
DR PDBsum; 7O1S; -.
DR PDBsum; 7O1T; -.
DR PDBsum; 7O25; -.
DR PDBsum; 7O26; -.
DR AlphaFoldDB; Q9X0Z6; -.
DR SMR; Q9X0Z6; -.
DR STRING; 243274.THEMA_07990; -.
DR EnsemblBacteria; AAD36344; AAD36344; TM_1269.
DR EnsemblBacteria; AGL50198; AGL50198; Tmari_1274.
DR KEGG; tma:TM1269; -.
DR KEGG; tmi:THEMA_07990; -.
DR KEGG; tmm:Tmari_1274; -.
DR KEGG; tmw:THMA_1294; -.
DR PATRIC; fig|243274.17.peg.1272; -.
DR eggNOG; COG0502; Bacteria.
DR InParanoid; Q9X0Z6; -.
DR OMA; IMGFNPY; -.
DR OrthoDB; 940969at2; -.
DR EvolutionaryTrace; Q9X0Z6; -.
DR Proteomes; UP000008183; Chromosome.
DR Proteomes; UP000013901; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0016740; F:transferase activity; IBA:GO_Central.
DR GO; GO:0044271; P:cellular nitrogen compound biosynthetic process; IEA:UniProt.
DR GO; GO:0018130; P:heterocycle biosynthetic process; IEA:UniProt.
DR GO; GO:1901362; P:organic cyclic compound biosynthetic process; IEA:UniProt.
DR GO; GO:1901566; P:organonitrogen compound biosynthetic process; IEA:UniProt.
DR GO; GO:0044272; P:sulfur compound biosynthetic process; IEA:UniProt.
DR GO; GO:0042364; P:water-soluble vitamin biosynthetic process; IEA:UniProt.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR010722; BATS_dom.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR024021; FeFe-hyd_HydE_rSAM.
DR InterPro; IPR034422; HydE/PylB-like.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR43726; PTHR43726; 1.
DR Pfam; PF06968; BATS; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR SFLD; SFLDF00348; FeFe_hydrogenase_maturase_(Hyd; 1.
DR SMART; SM00876; BATS; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR03956; rSAM_HydE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; 4Fe-4S; Iron; Iron-sulfur; Metal-binding;
KW Oxidoreductase; Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..348
FT /note="[FeFe] hydrogenase maturase subunit HydE"
FT /id="PRO_0000433230"
FT DOMAIN 49..268
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 63
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PIRSR:PIRSR004762-1,
FT ECO:0000269|PubMed:16137685, ECO:0000269|PubMed:18400755,
FT ECO:0000269|PubMed:19706452, ECO:0007744|PDB:3CIW,
FT ECO:0007744|PDB:3CIX, ECO:0007744|PDB:3IIX"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PIRSR:PIRSR004762-1,
FT ECO:0000269|PubMed:16137685, ECO:0007744|PDB:3CIW,
FT ECO:0007744|PDB:3CIX, ECO:0007744|PDB:3IIX"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PIRSR:PIRSR004762-1,
FT ECO:0000269|PubMed:16137685, ECO:0007744|PDB:3CIW,
FT ECO:0007744|PDB:3CIX, ECO:0007744|PDB:3IIX"
FT BINDING 311
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0007744|PDB:3CIX, ECO:0007744|PDB:3IIZ,
FT ECO:0007744|PDB:4JXC, ECO:0007744|PDB:4JY8,
FT ECO:0007744|PDB:4JY9, ECO:0007744|PDB:4JYE"
FT BINDING 319
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0007744|PDB:3CIX, ECO:0007744|PDB:4JY8,
FT ECO:0007744|PDB:4JY9, ECO:0007744|PDB:4JYE"
FT BINDING 322
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0007744|PDB:3CIX, ECO:0007744|PDB:4JY8,
FT ECO:0007744|PDB:4JY9, ECO:0007744|PDB:4JYE"
FT MUTAGEN 63
FT /note="C->A: Eliminates binding of one iron-sulfur cluster;
FT when associated with A-67 and A-70."
FT /evidence="ECO:0000269|PubMed:16137685"
FT MUTAGEN 67
FT /note="C->A: Eliminates binding of one iron-sulfur cluster;
FT when associated with A-63 and A-70."
FT /evidence="ECO:0000269|PubMed:16137685"
FT MUTAGEN 70
FT /note="C->A: Eliminates binding of one iron-sulfur cluster;
FT when associated with A-63 and A-67."
FT /evidence="ECO:0000269|PubMed:16137685"
FT HELIX 3..11
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 17..25
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 29..47
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 49..60
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 86..98
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 102..109
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 117..127
FT /evidence="ECO:0007829|PDB:5FEW"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:7O1O"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 142..151
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 165..171
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 177..189
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 193..196
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 207..220
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:5FEW"
FT TURN 237..240
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 246..259
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 269..274
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 278..283
FT /evidence="ECO:0007829|PDB:5FEW"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:5FEW"
FT TURN 297..299
FT /evidence="ECO:0007829|PDB:5FEW"
FT HELIX 300..302
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 305..308
FT /evidence="ECO:0007829|PDB:5FF3"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:5FEW"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:7O1P"
FT HELIX 319..329
FT /evidence="ECO:0007829|PDB:5FEW"
SQ SEQUENCE 348 AA; 39799 MW; 472505213FF63799 CRC64;
MTGREILEKL ERREFTREVL KEALSINDRG FNEALFKLAD EIRRKYVGDE VHIRAIIEFS
NVCRKNCLYC GLRRDNKNLK RYRMTPEEIV ERARLAVQFG AKTIVLQSGE DPYYMPDVIS
DIVKEIKKMG VAVTLSLGEW PREYYEKWKE AGADRYLLRH ETANPVLHRK LRPDTSFENR
LNCLLTLKEL GYETGAGSMV GLPGQTIDDL VDDLLFLKEH DFDMVGIGPF IPHPDTPLAN
EKKGDFTLTL KMVALTRILL PDSNIPATTA MGTIVPGGRE ITLRCGANVI MPNWTPSPYR
QLYQLYPGKI CVFEKDTACI PCVMKMIELL GRKPGRDWGG RKRVFETV
