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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
 
 
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