NIRDL_HYDTT
ID NIRDL_HYDTT Reviewed; 334 AA.
AC D3DFS4;
DT 12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT 23-MAR-2010, sequence version 1.
DT 25-MAY-2022, entry version 68.
DE RecName: Full=Siroheme decarboxylase {ECO:0000303|PubMed:25083922};
DE EC=4.1.1.111 {ECO:0000269|PubMed:25083922};
GN Name=nirDL {ECO:0000303|PubMed:25083922};
GN OrderedLocusNames=HTH_0209 {ECO:0000312|EMBL:BAI68676.1};
OS Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Hydrogenobacter.
OX NCBI_TaxID=608538;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 6534 / IAM 12695 / TK-6;
RX PubMed=20348262; DOI=10.1128/jb.00158-10;
RA Arai H., Kanbe H., Ishii M., Igarashi Y.;
RT "Complete genome sequence of the thermophilic, obligately
RT chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter
RT thermophilus TK-6.";
RL J. Bacteriol. 192:2651-2652(2010).
RN [2] {ECO:0007744|PDB:4CH7, ECO:0007744|PDB:4CZC}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND MUTAGENESIS OF
RP HIS-93; TYR-95; ARG-218; ARG-219; HIS-226; HIS-261 AND TYR-263.
RX PubMed=25083922; DOI=10.1016/j.jmb.2014.07.021;
RA Haufschildt K., Schmelz S., Kriegler T.M., Neumann A., Streif J., Arai H.,
RA Heinz D.W., Layer G.;
RT "The crystal structure of siroheme decarboxylase in complex with iron-
RT uroporphyrin III reveals two essential histidine residues.";
RL J. Mol. Biol. 426:3272-3286(2014).
CC -!- FUNCTION: Involved in heme d1 biosynthesis. Catalyzes the
CC decarboxylation of siroheme into didecarboxysiroheme. Siroheme is
CC probably decarboxylated to monodecarboxysiroheme, which is in turn
CC decarboxylated to didecarboxysiroheme. {ECO:0000269|PubMed:25083922}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H(+) + siroheme = 12,18-didecarboxysiroheme + 2 CO2;
CC Xref=Rhea:RHEA:19093, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:60052, ChEBI:CHEBI:140497; EC=4.1.1.111;
CC Evidence={ECO:0000269|PubMed:25083922};
CC -!- PATHWAY: Porphyrin-containing compound metabolism.
CC {ECO:0000305|PubMed:25083922}.
CC -!- MISCELLANEOUS: H.thermophilus possesses the fused nirDL gene but lacks
CC the genes encoding NirG and NirH. {ECO:0000305|PubMed:25083922}.
CC -!- SIMILARITY: Belongs to the Ahb/Nir family. {ECO:0000305}.
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DR EMBL; AP011112; BAI68676.1; -; Genomic_DNA.
DR RefSeq; WP_012962859.1; NC_017161.1.
DR PDB; 4CH7; X-ray; 2.00 A; A=1-334.
DR PDB; 4CZC; X-ray; 2.90 A; A=1-334.
DR PDBsum; 4CH7; -.
DR PDBsum; 4CZC; -.
DR AlphaFoldDB; D3DFS4; -.
DR SMR; D3DFS4; -.
DR STRING; 608538.HTH_0209; -.
DR EnsemblBacteria; BAI68676; BAI68676; HTH_0209.
DR KEGG; hth:HTH_0209; -.
DR PATRIC; fig|608538.5.peg.209; -.
DR eggNOG; COG1522; Bacteria.
DR OMA; PGVSHNY; -.
DR OrthoDB; 1844486at2; -.
DR BRENDA; 4.1.1.111; 2722.
DR Proteomes; UP000002574; Chromosome.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR040523; AsnC_trans_reg2.
DR InterPro; IPR019888; Tscrpt_reg_AsnC-like.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF17805; AsnC_trans_reg2; 2.
DR SMART; SM00344; HTH_ASNC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Reference proteome.
FT CHAIN 1..334
FT /note="Siroheme decarboxylase"
FT /id="PRO_0000450514"
FT ACT_SITE 93
FT /evidence="ECO:0000305|PubMed:25083922"
FT MUTAGEN 93
FT /note="H->A,S: Loss of activity. Does not alter binding of
FT the substrate analog Fe-URO III."
FT /evidence="ECO:0000269|PubMed:25083922"
FT MUTAGEN 93
FT /note="H->Q: Almost loss of activity. Does not alter
FT binding of the substrate analog Fe-URO III."
FT MUTAGEN 95
FT /note="Y->L: Does not affect didecarboxysiroheme
FT production. Shows a reduced ability to bind the substrate
FT analog Fe-URO III."
FT MUTAGEN 218
FT /note="R->A: Does not affect didecarboxysiroheme
FT production. Shows a reduced ability to bind the substrate
FT analog Fe-URO III."
FT MUTAGEN 218
FT /note="R->K: Does not affect didecarboxysiroheme
FT production. Does not alter binding of the substrate analog
FT Fe-URO III."
FT MUTAGEN 219
FT /note="R->Q: Does not affect didecarboxysiroheme
FT production. Shows a reduced ability to bind the substrate
FT analog Fe-URO III."
FT MUTAGEN 226
FT /note="H->Q: Does not affect didecarboxysiroheme
FT production. Cannot bind the substrate analog Fe-URO III."
FT MUTAGEN 261
FT /note="H->A,S: Loss of activity. Abolishes binding of the
FT substrate analog Fe-URO III."
FT /evidence="ECO:0000269|PubMed:25083922"
FT MUTAGEN 263
FT /note="Y->F: Does not affect didecarboxysiroheme
FT production. Shows a reduced ability to bind the substrate
FT analog Fe-URO III."
FT HELIX 4..11
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:4CZC"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 34..46
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 52..57
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 65..71
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 75..87
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 91..101
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 103..109
FT /evidence="ECO:0007829|PDB:4CH7"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 116..126
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 170..179
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 191..196
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 201..213
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 216..223
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 233..239
FT /evidence="ECO:0007829|PDB:4CH7"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 246..254
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 259..264
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 275..283
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 284..297
FT /evidence="ECO:0007829|PDB:4CH7"
FT STRAND 303..314
FT /evidence="ECO:0007829|PDB:4CH7"
FT HELIX 323..334
FT /evidence="ECO:0007829|PDB:4CH7"
SQ SEQUENCE 334 AA; 38862 MW; 8B5F9E6D4B822CFC CRC64;
MGNEFDKILK IIQKDIPLVK EPFSVLAQEV GIEEGKLLKT IEKLVEDGIV RHIAPIYDSR
LLGYDSALIA FKVDRQKLEE VANFVNACPG VSHNYERTHD FNLWFTLAVP PEISELEDVV
RLMAERERVK DYLVLRVVRL FKIGVKLDYE SPAEKESVDT KVYTYTPLTE EEKRIVSITQ
GSFPLVERPF LEYAKRLRMS EEELLEKLSA LKERGVLRRI SAVLYHRRAG YVANAMSVWE
VPEDAIEEVG RYIAGFKGVS HCYQRTTSEK FRYNLFAMMH GKGQEEIKLL AETISREKAL
SKYALLFSTR EFKKVRIKYF SEEFERWFKE LISA
