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