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BIOU_SYNY3
ID   BIOU_SYNY3              Reviewed;         331 AA.
AC   Q55650;
DT   12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   03-AUG-2022, entry version 116.
DE   RecName: Full=(S)-8-amino-7-oxononanoate synthase BioU {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000305};
DE            EC=2.6.1.- {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000269|PubMed:32042199};
DE   AltName: Full=8-amino-7-oxononanoate carboxylating dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000305};
GN   Name=bioU {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000303|PubMed:32042199};
GN   OrderedLocusNames=slr0355;
OS   Synechocystis sp. (strain PCC 6803 / Kazusa).
OC   Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC   unclassified Synechocystis.
OX   NCBI_TaxID=1111708;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=PCC 6803 / Kazusa;
RX   PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA   Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA   Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA   Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA   Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence analysis of the genome of the unicellular cyanobacterium
RT   Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT   genome and assignment of potential protein-coding regions.";
RL   DNA Res. 3:109-136(1996).
RN   [2] {ECO:0007744|PDB:6IR4, ECO:0007744|PDB:6ITD, ECO:0007744|PDB:6K36, ECO:0007744|PDB:6K37, ECO:0007744|PDB:6K38}
RP   X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 2-331, X-RAY CRYSTALLOGRAPHY
RP   (1.78 ANGSTROMS) OF CONJUGATES AND MUTANTS, X-RAY CRYSTALLOGRAPHY (2.50
RP   ANGSTROMS) IN COMPLEX WITH NAD, PROTEIN SEQUENCE OF 121-137, FUNCTION,
RP   CATALYTIC ACTIVITY, REACTION MECHANISM, ACTIVE SITE, EXPRESSION IN E.COLI,
RP   SUBUNIT, MASS SPECTROMETRY, DISRUPTION PHENOTYPE, ALLYSINE AT LYS-124, AND
RP   MUTAGENESIS OF LYS-124; HIS-233 AND ASP-235.
RC   STRAIN=PCC 6803 / Kazusa;
RX   PubMed=32042199; DOI=10.1038/s41589-019-0461-9;
RA   Sakaki K., Ohishi K., Shimizu T., Kobayashi I., Mori N., Matsuda K.,
RA   Tomita T., Watanabe H., Tanaka K., Kuzuyama T., Nishiyama M.;
RT   "A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in
RT   cyanobacteria.";
RL   Nat. Chem. Biol. 16:415-422(2020).
CC   -!- FUNCTION: A 'suicide' enzyme that participates in biotin synthesis.
CC       Catalyzes the formation of (S)-8-amino-7-oxononanoate (DAN-carbamic
CC       acid) from (7R,8S)-8-amino-7-(carboxyamino)nonanoate (DAN), a function
CC       equivalent to the cannonical BioA reaction and the first half-reaction
CC       of BioD. The cellular requirement for biotin is thought be low enough
CC       that this single turnover enzyme supplies a sufficient amount of the
CC       cofactor. Overall it catalyzes three reactions: formation of a covalent
CC       linkage with 8-amino-7-oxononanoate to yield a BioU-DAN conjugate at
CC       the epsilon-amino group of Lys124 of BioU using NAD(P)H, carboxylation
CC       of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-
CC       carbamic acid using NAD(P)+ (By similarity) (PubMed:32042199). A
CC       coupled Synechocystis BioU/BioD assay produces dethiobiotin from DAN.
CC       Complements a bioA deletion in E.coli but not a bioD1 deletion
CC       (PubMed:32042199). {ECO:0000255|HAMAP-Rule:MF_00852,
CC       ECO:0000269|PubMed:32042199}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(8S)-8-amino-7-oxononanoate + CO2 + L-lysyl-[protein] =
CC         (7R,8S)-8-amino-7-(carboxyamino)nonanoate + (S)-2-amino-6-
CC         oxohexanoyl-[protein] + 2 H(+); Xref=Rhea:RHEA:63660, Rhea:RHEA-
CC         COMP:9752, Rhea:RHEA-COMP:12448, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:16526, ChEBI:CHEBI:29969, ChEBI:CHEBI:131803,
CC         ChEBI:CHEBI:149468, ChEBI:CHEBI:149470; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00852, ECO:0000269|PubMed:32042199};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63661;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(8S)-8-amino-7-oxononanoate + H(+) + L-lysyl-[protein] + NADPH
CC         = H2O + N(6)-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-lysyl-[protein]
CC         + NADP(+); Xref=Rhea:RHEA:63664, Rhea:RHEA-COMP:9752, Rhea:RHEA-
CC         COMP:16405, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969,
CC         ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:149468,
CC         ChEBI:CHEBI:149472; Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000305|PubMed:32042199};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63665;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=CO2 + H2O + N(6)-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-
CC         lysyl-[protein] + NADP(+) = (7R,8S)-8-amino-7-(carboxyamino)nonanoate
CC         + (S)-2-amino-6-oxohexanoyl-[protein] + 3 H(+) + NADPH;
CC         Xref=Rhea:RHEA:63668, Rhea:RHEA-COMP:12448, Rhea:RHEA-COMP:16405,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:131803,
CC         ChEBI:CHEBI:149470, ChEBI:CHEBI:149472; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00852, ECO:0000305|PubMed:32042199};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63669;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(8S)-8-amino-7-oxononanoate + H(+) + L-lysyl-[protein] + NADH
CC         = H2O + N(6)-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-lysyl-[protein]
CC         + NAD(+); Xref=Rhea:RHEA:63672, Rhea:RHEA-COMP:9752, Rhea:RHEA-
CC         COMP:16405, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969,
CC         ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:149468,
CC         ChEBI:CHEBI:149472; Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63673;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=CO2 + H2O + N(6)-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-
CC         lysyl-[protein] + NAD(+) = (7R,8S)-8-amino-7-(carboxyamino)nonanoate
CC         + (S)-2-amino-6-oxohexanoyl-[protein] + 3 H(+) + NADH;
CC         Xref=Rhea:RHEA:63676, Rhea:RHEA-COMP:12448, Rhea:RHEA-COMP:16405,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:131803,
CC         ChEBI:CHEBI:149470, ChEBI:CHEBI:149472; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00852, ECO:0000269|PubMed:32042199};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63677;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00852,
CC         ECO:0000269|PubMed:32042199};
CC   -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000269|PubMed:32042199}.
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00852,
CC       ECO:0000269|PubMed:32042199}.
CC   -!- DOMAIN: Has 2 domains; discontinuous domain I (residues 1-149 and 291-
CC       331) forms a nucleotide-binding domain while domain II (residues 150-
CC       290) binds substrate. {ECO:0000269|PubMed:32042199}.
CC   -!- MASS SPECTROMETRY: Mass=37805; Method=Electrospray; Note=For native
CC       protein.; Evidence={ECO:0000269|PubMed:32042199};
CC   -!- MASS SPECTROMETRY: Mass=37976; Method=Electrospray; Note=For 7,8-
CC       diaminononanoate acid-protein (DAN) conjugate, a reaction
CC       intermediate.; Evidence={ECO:0000269|PubMed:32042199};
CC   -!- DISRUPTION PHENOTYPE: Loss of biotin biosynthesis.
CC       {ECO:0000269|PubMed:32042199}.
CC   -!- MISCELLANEOUS: In canonical biotin synthesis a pimeloyl-conjugate is
CC       transformed into biotin by the subsequent action of BioF, BioA, BioD
CC       and BioB. This enzyme replaces BioA and performs the first half-
CC       reaction of BioD. In Synechocystis BioD acts on the product of this
CC       enzyme. {ECO:0000255|HAMAP-Rule:MF_00852, ECO:0000269|PubMed:32042199}.
CC   -!- SIMILARITY: Belongs to the BioU family. {ECO:0000255|HAMAP-
CC       Rule:MF_00852}.
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DR   EMBL; BA000022; BAA10170.1; -; Genomic_DNA.
DR   PIR; S76318; S76318.
DR   PDB; 6IR4; X-ray; 2.00 A; A=2-331.
DR   PDB; 6ITD; X-ray; 2.00 A; A=1-331.
DR   PDB; 6K36; X-ray; 2.30 A; A=1-331.
DR   PDB; 6K37; X-ray; 2.50 A; A=1-331.
DR   PDB; 6K38; X-ray; 1.78 A; A=1-331.
DR   PDBsum; 6IR4; -.
DR   PDBsum; 6ITD; -.
DR   PDBsum; 6K36; -.
DR   PDBsum; 6K37; -.
DR   PDBsum; 6K38; -.
DR   AlphaFoldDB; Q55650; -.
DR   SMR; Q55650; -.
DR   IntAct; Q55650; 1.
DR   STRING; 1148.1001543; -.
DR   PaxDb; Q55650; -.
DR   EnsemblBacteria; BAA10170; BAA10170; BAA10170.
DR   KEGG; syn:slr0355; -.
DR   eggNOG; COG1748; Bacteria.
DR   InParanoid; Q55650; -.
DR   OMA; MAANVCG; -.
DR   BioCyc; MetaCyc:MON-21139; -.
DR   UniPathway; UPA00078; -.
DR   Proteomes; UP000001425; Chromosome.
DR   GO; GO:0051287; F:NAD binding; IDA:UniProtKB.
DR   GO; GO:0050661; F:NADP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR   GO; GO:0008483; F:transaminase activity; IEA:UniProtKB-KW.
DR   GO; GO:0009102; P:biotin biosynthetic process; IDA:UniProtKB.
DR   GO; GO:0006520; P:cellular amino acid metabolic process; IEA:InterPro.
DR   HAMAP; MF_00852; BioU; 1.
DR   InterPro; IPR044262; BioU-like.
DR   InterPro; IPR006096; Glu/Leu/Phe/Val_DH_C.
DR   InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR   Pfam; PF00208; ELFV_dehydrog; 1.
DR   SUPFAM; SSF51735; SSF51735; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Aminotransferase; Biotin biosynthesis;
KW   Direct protein sequencing; NAD; NADP; Nucleotide-binding;
KW   Reference proteome; Transferase.
FT   CHAIN           1..331
FT                   /note="(S)-8-amino-7-oxononanoate synthase BioU"
FT                   /id="PRO_0000450575"
FT   ACT_SITE        124
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000269|PubMed:32042199"
FT   ACT_SITE        194
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000305|PubMed:32042199"
FT   ACT_SITE        198
FT                   /note="Proton donor and proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000305|PubMed:32042199"
FT   BINDING         15..19
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000269|PubMed:32042199, ECO:0007744|PDB:6K37"
FT   BINDING         60
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000269|PubMed:32042199, ECO:0007744|PDB:6K37"
FT   BINDING         190..191
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000269|PubMed:32042199, ECO:0007744|PDB:6K37"
FT   MOD_RES         124
FT                   /note="Allysine"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00852,
FT                   ECO:0000269|PubMed:32042199"
FT   MUTAGEN         124
FT                   /note="K->A,R: No longer forms a BioU-DAN conjugate."
FT                   /evidence="ECO:0000269|PubMed:32042199"
FT   MUTAGEN         233
FT                   /note="H->A: Decreased product formation, still able to
FT                   form a BioU-DAN conjugate."
FT                   /evidence="ECO:0000269|PubMed:32042199"
FT   MUTAGEN         235
FT                   /note="D->N: Decreased product formation, able to weakly
FT                   form a BioU-DAN conjugate."
FT                   /evidence="ECO:0000269|PubMed:32042199"
FT   STRAND          9..14
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           18..27
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          31..40
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          43..46
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           53..63
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           66..68
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          72..74
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           78..85
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          89..93
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           102..113
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          117..121
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           126..134
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           136..142
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          144..149
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   TURN            152..154
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           156..164
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           165..167
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          169..181
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           186..189
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           192..196
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           204..208
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           212..220
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   TURN            221..224
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          225..228
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           235..241
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           247..249
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          250..257
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          268..274
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          280..286
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   HELIX           293..313
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   STRAND          318..321
FT                   /evidence="ECO:0007829|PDB:6K38"
FT   TURN            322..324
FT                   /evidence="ECO:0007829|PDB:6K38"
SQ   SEQUENCE   331 AA;  35387 MW;  40FD0B61DEE97A00 CRC64;
     MENNSLAPLR VGILGFGGLG QAAARLLAPK QEMKLVAVAD RHGYLYDADG IDVDNAVQAY
     TQQGSVGKAK KGQMSEQSIE DLIGEGEVDG YFLALPNLPN TFMADVTRQF IASGWQGVLV
     DALKRTSAVE QLITLREDLA QAGITYMTGC GATPGLLTAA AAIASQSFQE IHQVKITFGV
     GIANWEAYRA TIREDIAHMP GYNVDKAQAM TDAEVAALLD QTNGILALED MEHADDIMLE
     LAGICHRDQV TVGGVVDTRN PKKPLSTHVK ITGRTFEGKI SSHTFTLGDE TSMAANVCGP
     AFGYLKAGYG LHRQGLKGLF TAADVMPKFV R
 
 
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