DSD_PSEPK
ID DSD_PSEPK Reviewed; 635 AA.
AC Q88JU3;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=3-dehydroshikimate dehydratase {ECO:0000303|PubMed:27706847};
DE Short=DSD {ECO:0000303|PubMed:27706847};
DE EC=4.2.1.118 {ECO:0000269|PubMed:27706847};
GN Name=quiC1 {ECO:0000303|PubMed:27706847};
GN Synonyms=quiC {ECO:0000312|EMBL:AAN68163.1};
GN OrderedLocusNames=PP_2554 {ECO:0000312|EMBL:AAN68163.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2] {ECO:0007744|PDB:5HMQ}
RP X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DOMAIN, SUBUNIT, AND
RP MUTAGENESIS OF HIS-168 AND SER-206.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=27706847; DOI=10.1111/mmi.13542;
RA Peek J., Roman J., Moran G.R., Christendat D.;
RT "Structurally diverse dehydroshikimate dehydratase variants participate in
RT microbial quinate catabolism.";
RL Mol. Microbiol. 103:39-54(2017).
CC -!- FUNCTION: Catalyzes the conversion of 3-dehydroshikimate to
CC protocatechuate (3,4-dihydroxybenzoate), a common intermediate of
CC quinate and shikimate degradation pathways.
CC {ECO:0000269|PubMed:27706847}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-dehydroshikimate = 3,4-dihydroxybenzoate + H2O;
CC Xref=Rhea:RHEA:24848, ChEBI:CHEBI:15377, ChEBI:CHEBI:16630,
CC ChEBI:CHEBI:36241; EC=4.2.1.118;
CC Evidence={ECO:0000269|PubMed:27706847};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24849;
CC Evidence={ECO:0000305|PubMed:27706847};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:27706847};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:27706847};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27706847};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:27706847};
CC Note=Requires a divalent metal cation for DSD activity, with a
CC preference for Co(2+) but can also use Ni(2+), Mn(2+) and Mg(2+).
CC {ECO:0000269|PubMed:27706847};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=331 uM for 3-dehydroshikimate {ECO:0000269|PubMed:27706847};
CC Note=kcat is 163.6 sec(-1). {ECO:0000269|PubMed:27706847};
CC -!- PATHWAY: Aromatic compound metabolism; 3,4-dihydroxybenzoate
CC biosynthesis. {ECO:0000269|PubMed:27706847}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:27706847}.
CC -!- DOMAIN: Consists of a fusion of two distinct domains: an N-terminal
CC sugar phosphate isomerase-like domain associated with DSD activity and
CC a C-terminal hydroxyphenyl-pyruvate dioxygenase-like domain. This C-
CC terminal domain does not show any 4-hydroxyphenylpyruvate dioxygenase
CC (HPPD) or protocatechuate dioxygenase (PCD) activity, but appears to be
CC important for optimal DSD activity of QuiC1 in vivo.
CC {ECO:0000269|PubMed:27706847}.
CC -!- SIMILARITY: Belongs to the bacterial two-domain DSD family.
CC {ECO:0000255|HAMAP-Rule:MF_02238, ECO:0000305|PubMed:27706847}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE015451; AAN68163.1; -; Genomic_DNA.
DR RefSeq; NP_744699.1; NC_002947.4.
DR RefSeq; WP_003250790.1; NC_002947.4.
DR PDB; 5HMQ; X-ray; 2.37 A; A/B/C/D/E/F=1-635.
DR PDBsum; 5HMQ; -.
DR AlphaFoldDB; Q88JU3; -.
DR SMR; Q88JU3; -.
DR STRING; 160488.PP_2554; -.
DR EnsemblBacteria; AAN68163; AAN68163; PP_2554.
DR KEGG; ppu:PP_2554; -.
DR PATRIC; fig|160488.4.peg.2713; -.
DR eggNOG; COG1082; Bacteria.
DR eggNOG; COG3185; Bacteria.
DR HOGENOM; CLU_029438_0_0_6; -.
DR OMA; FPGQGEF; -.
DR PhylomeDB; Q88JU3; -.
DR BioCyc; PPUT160488:G1G01-2737-MON; -.
DR UniPathway; UPA00088; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0046565; F:3-dehydroshikimate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0046279; P:3,4-dihydroxybenzoate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019631; P:quinate catabolic process; ISS:UniProtKB.
DR GO; GO:0019633; P:shikimate catabolic process; ISS:UniProtKB.
DR CDD; cd08342; HPPD_N_like; 1.
DR Gene3D; 3.10.180.10; -; 2.
DR HAMAP; MF_02238; DSD; 1.
DR InterPro; IPR041736; 4OHPhenylPyrv_dOase_N.
DR InterPro; IPR043700; DSD.
DR InterPro; IPR029068; Glyas_Bleomycin-R_OHBP_Dase.
DR InterPro; IPR004360; Glyas_Fos-R_dOase_dom.
DR InterPro; IPR037523; VOC.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR Pfam; PF00903; Glyoxalase; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
DR SUPFAM; SSF54593; SSF54593; 1.
DR PROSITE; PS51819; VOC; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Lyase; Magnesium; Manganese; Metal-binding; Nickel;
KW Reference proteome.
FT CHAIN 1..635
FT /note="3-dehydroshikimate dehydratase"
FT /id="PRO_0000448878"
FT DOMAIN 295..414
FT /note="VOC 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01163"
FT DOMAIN 440..590
FT /note="VOC 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01163"
FT BINDING 134
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 165
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 191
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 239
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 443
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 521
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT BINDING 599
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27706847,
FT ECO:0007744|PDB:5HMQ"
FT MUTAGEN 168
FT /note="H->A: 21-fold decrease in turnover rate."
FT /evidence="ECO:0000269|PubMed:27706847"
FT MUTAGEN 206
FT /note="S->A: 10-fold decrease in the affinity for
FT dehydroshikimate without significantly altering the
FT turnover rate."
FT /evidence="ECO:0000269|PubMed:27706847"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 33..38
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 43..53
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 56..65
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 74..91
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 110..127
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 145..155
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 166..170
FT /evidence="ECO:0007829|PDB:5HMQ"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 176..181
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 187..192
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 202..209
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 215..218
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 220..229
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 250..274
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 293..302
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 305..317
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 321..336
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 347..349
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 350..358
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 359..370
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 372..381
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 396..398
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 400..402
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 408..413
FT /evidence="ECO:0007829|PDB:5HMQ"
FT TURN 416..419
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 422..425
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 426..428
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 440..448
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 450..452
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 453..463
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 482..487
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 491..499
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 503..508
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 517..525
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 529..539
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 548..557
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 564..570
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 574..577
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 583..589
FT /evidence="ECO:0007829|PDB:5HMQ"
FT STRAND 597..603
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 612..614
FT /evidence="ECO:0007829|PDB:5HMQ"
FT HELIX 615..624
FT /evidence="ECO:0007829|PDB:5HMQ"
SQ SEQUENCE 635 AA; 70407 MW; 13695617CA91B46B CRC64;
MQRSIATVSL SGTLPEKLEA IAAAGFDGVE IFENDLLYYA GSPRQVRQMC ADLGIAITLF
QPFRDFEGCR RDRLQKNLDR AERKFDLMQE LGTDLVLVCS NVQADALGDE QLLVDDLRLL
GEHAGKRGLR IGYEALAWGR HVNTYQQVWN LVRQADHPAL GVILDSFHTL SLKGDPSAIR
DIPGDKIFFV QMADAPILAM DVLEWSRHFR CFPGQGEMDM AGFLAPILAT GYRGPLSLEI
FNDGFRAAPT RQNAADGLRS LLYLEEQTRL RLEQENTPIE PGVLFSPPPA SAYDGVEFLE
FAVDEAVGAR LGNWLKRLGF AEAGKHRSKE VQLLRQGDIN IVLNAEPYSF GHNFFEAHGP
SLCATALRVK DQQAALKRAT AFRGQPFRGL VGPNECEVPA VRAPDGSLLY LVEQGTAGHT
LYDTDFSLDN NATATGGLRR IDHMALALPA ESLDSWVLFY KSLFDFAADD EVVLPDPYGL
VKSRALRSQC GTLRLPLNIS ENRNTAIAHA LSSYRGSGVH HIAFDCDDIF REVARAKLAG
VPLLEIPLNY YDDLAARFDF DDEFLSELAY YNVLYDRDAQ GGELFHVYTE PFEERFFFEI
IQRKAGYAGY GAANVAVRLA AMAKARSGAA RKPVL
