KDNB_SHEON
ID KDNB_SHEON Reviewed; 356 AA.
AC Q8EEB0;
DT 11-NOV-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=3-deoxy-alpha-D-manno-octulosonate 8-oxidase {ECO:0000305};
DE EC=1.1.3.48 {ECO:0000269|PubMed:23413030};
GN Name=kdnB {ECO:0000303|PubMed:23413030};
GN OrderedLocusNames=SO_2477 {ECO:0000312|EMBL:AAN55508.1};
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, PATHWAY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=MR-1;
RX PubMed=23413030; DOI=10.1074/jbc.m113.453324;
RA Gattis S.G., Chung H.S., Trent M.S., Raetz C.R.;
RT "The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the
RT lipopolysaccharide of Shewanella oneidensis.";
RL J. Biol. Chem. 288:9216-9225(2013).
CC -!- FUNCTION: Catalyzes the first step of the biosynthesis of Kdo8N (8-
CC amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-
CC octulosonate). {ECO:0000269|PubMed:23413030}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-deoxy-alpha-D-manno-oct-2-ulosonate + O2 = 3,8-dideoxy-8-
CC oxo-alpha-D-manno-octulosonate + H2O2; Xref=Rhea:RHEA:46888,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:85986,
CC ChEBI:CHEBI:87090; EC=1.1.3.48;
CC Evidence={ECO:0000269|PubMed:23413030};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:23413030};
CC Note=Shows highest activity with Mn(2+) and Fe(2+).
CC {ECO:0000269|PubMed:23413030};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:23413030}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; lipopolysaccharide
CC biosynthesis. {ECO:0000269|PubMed:23413030}.
CC -!- DISRUPTION PHENOTYPE: A double kdnA/kdnB deletion mutant shows
CC increased sensitivity to polymyxin B and bile salts.
CC {ECO:0000269|PubMed:23413030}.
CC -!- MISCELLANEOUS: Kdo8N is found in lipopolysaccharides of members of the
CC Shewanella genus. {ECO:0000305|PubMed:23413030}.
CC -!- SIMILARITY: Belongs to the iron-containing alcohol dehydrogenase
CC family. {ECO:0000305}.
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DR EMBL; AE014299; AAN55508.1; -; Genomic_DNA.
DR RefSeq; NP_718064.1; NC_004347.2.
DR RefSeq; WP_011072443.1; NZ_CP053946.1.
DR PDB; 5K8C; X-ray; 1.85 A; A=1-356.
DR PDBsum; 5K8C; -.
DR AlphaFoldDB; Q8EEB0; -.
DR SMR; Q8EEB0; -.
DR STRING; 211586.SO_2477; -.
DR PaxDb; Q8EEB0; -.
DR KEGG; son:SO_2477; -.
DR PATRIC; fig|211586.12.peg.2386; -.
DR eggNOG; COG1454; Bacteria.
DR HOGENOM; CLU_773153_0_0_6; -.
DR OMA; MMASYMG; -.
DR OrthoDB; 1456634at2; -.
DR PhylomeDB; Q8EEB0; -.
DR BioCyc; MetaCyc:MON-19348; -.
DR BioCyc; SONE211586:G1GMP-2263-MON; -.
DR BRENDA; 1.1.3.48; 5706.
DR UniPathway; UPA00030; -.
DR Proteomes; UP000008186; Chromosome.
DR GO; GO:0004022; F:alcohol dehydrogenase (NAD+) activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR001670; ADH_Fe/GldA.
DR InterPro; IPR039697; Alcohol_dehydrogenase_Fe.
DR PANTHER; PTHR11496; PTHR11496; 1.
DR Pfam; PF00465; Fe-ADH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Iron; Lipopolysaccharide biosynthesis; Manganese;
KW Metal-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..356
FT /note="3-deoxy-alpha-D-manno-octulosonate 8-oxidase"
FT /id="PRO_0000434589"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 18..21
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 22..29
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 37..42
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 49..53
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 73..86
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 92..99
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 100..112
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 135..141
FT /evidence="ECO:0007829|PDB:5K8C"
FT TURN 146..148
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 157..164
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 166..168
FT /evidence="ECO:0007829|PDB:5K8C"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 177..180
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 185..203
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 210..228
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 234..247
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 248..251
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 256..268
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 272..280
FT /evidence="ECO:0007829|PDB:5K8C"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 288..300
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 315..326
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 329..336
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 340..342
FT /evidence="ECO:0007829|PDB:5K8C"
FT HELIX 346..355
FT /evidence="ECO:0007829|PDB:5K8C"
SQ SEQUENCE 356 AA; 39435 MW; 75227BD9D2E41C5B CRC64;
MSFKNFKVVE KMIFGRGSFV QLDDVLAAQR KADDDFVVFL VDDVHQGKPL EARIPVKAQD
LLIWVNVDEE PSTIQIDALT EQVQAFNGKL PVSVVGLGGG STMDVAKAVS LMLTNPGGSA
MYQGWDLIKK PAVHHIGIPT ISGTGAEASR TAVLCGPVRK LGLNSDYTVF DQIIMDSELI
DGVETDQWFY TGMDCYIHCV ESLEGTFLNE FSKAYAEKAM DLCRQVYLED HPEKDDKLMM
ASFMGGMSIA YSQVGACHAV SYGLSYILGY HHGIGNCIAF DVLEEFYPEG VAEFRLMMKK
HNITLPKNIC KDLPDETIAK MVAVTKSMGP LWANVYGPTW EEKVTDEMLT ALFRRI
