YDIB_SALTY
ID YDIB_SALTY Reviewed; 288 AA.
AC Q8ZPR4;
DT 19-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Quinate/shikimate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01578};
DE EC=1.1.1.282 {ECO:0000255|HAMAP-Rule:MF_01578};
DE AltName: Full=NAD-dependent shikimate 5-dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01578};
GN Name=ydiB {ECO:0000255|HAMAP-Rule:MF_01578}; OrderedLocusNames=STM1359;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NAD, AND SUBUNIT.
RA Minasov G., Light S.H., Halavaty A., Shuvalova L., Dubrovska I., Winsor J.,
RA Papazisi L., Anderson W.F.;
RT "1.95 angstrom crystal structure of shikimate 5-dehydrogenase (AroE) from
RT Salmonella enterica subsp. enterica serovar Typhimurium in complex with
RT NAD.";
RL Submitted (JUL-2011) to the PDB data bank.
CC -!- FUNCTION: The actual biological function of YdiB remains unclear, nor
CC is it known whether 3-dehydroshikimate or quinate represents the
CC natural substrate. Catalyzes the reversible NAD-dependent reduction of
CC both 3-dehydroshikimate (DHSA) and 3-dehydroquinate to yield shikimate
CC (SA) and quinate, respectively. It can use both NAD or NADP for
CC catalysis, however it has higher catalytic efficiency with NAD.
CC {ECO:0000255|HAMAP-Rule:MF_01578}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-quinate + NAD(+) = 3-dehydroquinate + H(+) + NADH;
CC Xref=Rhea:RHEA:22364, ChEBI:CHEBI:15378, ChEBI:CHEBI:29751,
CC ChEBI:CHEBI:32364, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.282; Evidence={ECO:0000255|HAMAP-Rule:MF_01578};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-quinate + NADP(+) = 3-dehydroquinate + H(+) + NADPH;
CC Xref=Rhea:RHEA:18425, ChEBI:CHEBI:15378, ChEBI:CHEBI:29751,
CC ChEBI:CHEBI:32364, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC EC=1.1.1.282; Evidence={ECO:0000255|HAMAP-Rule:MF_01578};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH;
CC Xref=Rhea:RHEA:17737, ChEBI:CHEBI:15378, ChEBI:CHEBI:16630,
CC ChEBI:CHEBI:36208, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC EC=1.1.1.282; Evidence={ECO:0000255|HAMAP-Rule:MF_01578};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + shikimate = 3-dehydroshikimate + H(+) + NADH;
CC Xref=Rhea:RHEA:17741, ChEBI:CHEBI:15378, ChEBI:CHEBI:16630,
CC ChEBI:CHEBI:36208, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.282; Evidence={ECO:0000255|HAMAP-Rule:MF_01578};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; chorismate biosynthesis;
CC chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step
CC 4/7. {ECO:0000255|HAMAP-Rule:MF_01578}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01578}.
CC -!- SIMILARITY: Belongs to the shikimate dehydrogenase family.
CC {ECO:0000255|HAMAP-Rule:MF_01578}.
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DR EMBL; AE006468; AAL20284.1; -; Genomic_DNA.
DR RefSeq; NP_460325.1; NC_003197.2.
DR RefSeq; WP_000383490.1; NC_003197.2.
DR PDB; 3T4E; X-ray; 1.95 A; A/B=1-288.
DR PDBsum; 3T4E; -.
DR AlphaFoldDB; Q8ZPR4; -.
DR SMR; Q8ZPR4; -.
DR STRING; 99287.STM1359; -.
DR PaxDb; Q8ZPR4; -.
DR EnsemblBacteria; AAL20284; AAL20284; STM1359.
DR GeneID; 1252877; -.
DR KEGG; stm:STM1359; -.
DR PATRIC; fig|99287.12.peg.1443; -.
DR HOGENOM; CLU_044063_4_4_6; -.
DR OMA; SIFARND; -.
DR PhylomeDB; Q8ZPR4; -.
DR BioCyc; SENT99287:STM1359-MON; -.
DR UniPathway; UPA00053; UER00087.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0030266; F:quinate 3-dehydrogenase (NAD+) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0052733; F:quinate 3-dehydrogenase (NADP+) activity; IEA:UniProtKB-EC.
DR GO; GO:0052734; F:shikimate 3-dehydrogenase (NAD+) activity; IEA:UniProtKB-EC.
DR GO; GO:0004764; F:shikimate 3-dehydrogenase (NADP+) activity; IBA:GO_Central.
DR GO; GO:0009073; P:aromatic amino acid family biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0008652; P:cellular amino acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009423; P:chorismate biosynthetic process; IBA:GO_Central.
DR GO; GO:0019632; P:shikimate metabolic process; IBA:GO_Central.
DR HAMAP; MF_00222; Shikimate_DH_AroE; 1.
DR HAMAP; MF_01578; Shikimate_DH_YdiB; 1.
DR InterPro; IPR046346; Aminiacid_DH-like_N_sf.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR022872; Quinate/Shikimate_DH.
DR InterPro; IPR041121; SDH_C.
DR InterPro; IPR013708; Shikimate_DH-bd_N.
DR InterPro; IPR022893; Shikimate_DH_fam.
DR PANTHER; PTHR21089; PTHR21089; 1.
DR Pfam; PF18317; SDH_C; 1.
DR Pfam; PF08501; Shikimate_dh_N; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF53223; SSF53223; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Aromatic amino acid biosynthesis;
KW NAD; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..288
FT /note="Quinate/shikimate dehydrogenase"
FT /id="PRO_0000136072"
FT BINDING 71
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578"
FT BINDING 107
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578"
FT BINDING 132..135
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578,
FT ECO:0000269|Ref.2"
FT BINDING 155..158
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578,
FT ECO:0000269|Ref.2"
FT BINDING 205
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578,
FT ECO:0000269|Ref.2"
FT BINDING 232..235
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578,
FT ECO:0000269|Ref.2"
FT BINDING 255
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01578,
FT ECO:0000269|Ref.2"
FT STRAND 8..15
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 22..33
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:3T4E"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 49..58
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 71..74
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 83..88
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 92..97
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 100..104
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 106..117
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 126..130
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 149..155
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 160..174
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 187..196
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 198..202
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 240..247
FT /evidence="ECO:0007829|PDB:3T4E"
FT STRAND 251..253
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 255..271
FT /evidence="ECO:0007829|PDB:3T4E"
FT HELIX 277..283
FT /evidence="ECO:0007829|PDB:3T4E"
SQ SEQUENCE 288 AA; 31337 MW; 42984154DE6BB962 CRC64;
MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPYTYM AFEVDNTTFA SAIEGLKALK
MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY LRGYNTDGTG HIRAIKESGF
DMRGKTMVLL GAGGAATAIG AQAAIEGIKE IKLFNRKDDF FEKAVAFAKR VNENTDCVVT
VTDLADQHAF TEALASADIL TNGTKVGMKP LENESLIGDV SLLRPELLVT ECVYNPHMTK
LLQQAQQAGC KTIDGYGMLL WQGAEQFELW TGKAFPLDYV KQVMGFTA
