PLYL_DICD3
ID PLYL_DICD3 Reviewed; 425 AA.
AC P0C1A7; E0SIP1; Q47473; Q59421;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2006, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Pectate lyase L;
DE EC=4.2.2.2 {ECO:0000269|PubMed:10368144, ECO:0000269|PubMed:8577252};
DE AltName: Full=Pectate transeliminase;
DE AltName: Full=Pel9A;
DE Flags: Precursor;
GN Name=pelL; OrderedLocusNames=Dda3937_02794;
OS Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937)).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Pectobacteriaceae; Dickeya.
OX NCBI_TaxID=198628;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP PH DEPENDENCE, INDUCTION, ROLE IN SOFT-ROT DISEASE, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=3937;
RX PubMed=8577252; DOI=10.1111/j.1365-2958.1995.tb02341.x;
RA Lojkowska E., Masclaux C., Boccara M., Robert-Baudouy J.,
RA Hugouvieux-Cotte-Pattat N.;
RT "Characterization of the pelL gene encoding a novel pectate lyase of
RT Erwinia chrysanthemi 3937.";
RL Mol. Microbiol. 16:1183-1195(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3937;
RX PubMed=21217001; DOI=10.1128/jb.01513-10;
RA Glasner J.D., Yang C.H., Reverchon S., Hugouvieux-Cotte-Pattat N.,
RA Condemine G., Bohin J.P., Van Gijsegem F., Yang S., Franza T., Expert D.,
RA Plunkett G. III, San Francisco M.J., Charkowski A.O., Py B., Bell K.,
RA Rauscher L., Rodriguez-Palenzuela P., Toussaint A., Holeva M.C., He S.Y.,
RA Douet V., Boccara M., Blanco C., Toth I., Anderson B.D., Biehl B.S.,
RA Mau B., Flynn S.M., Barras F., Lindeberg M., Birch P.R., Tsuyumu S.,
RA Shi X., Hibbing M., Yap M.N., Carpentier M., Dassa E., Umehara M.,
RA Kim J.F., Rusch M., Soni P., Mayhew G.F., Fouts D.E., Gill S.R.,
RA Blattner F.R., Keen N.T., Perna N.T.;
RT "Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937.";
RL J. Bacteriol. 193:2076-2077(2011).
RN [3]
RP CRYSTALLIZATION.
RC STRAIN=3937;
RX PubMed=9761915; DOI=10.1107/s0907444997012043;
RA Shevchik V., Scott M., Mayans O., Jenkins J.;
RT "Crystallization and preliminary X-ray analysis of a member of a new family
RT of pectate lyases, PelL from Erwinia chrysanthemi.";
RL Acta Crystallogr. D 54:419-422(1998).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10368144; DOI=10.1128/jb.181.12.3705-3709.1999;
RA Roy C., Kester H., Visser J., Shevchik V., Hugouvieux-Cotte-Pattat N.,
RA Robert-Baudouy J., Benen J.;
RT "Modes of action of five different endopectate lyases from Erwinia
RT chrysanthemi 3937.";
RL J. Bacteriol. 181:3705-3709(1999).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 26-425 IN COMPLEX WITH CALCIUM
RP IONS, ACTIVE SITE, CATALYTIC MECHANISM, AND MUTAGENESIS OF LYS-273.
RC STRAIN=3937;
RX PubMed=14670977; DOI=10.1074/jbc.m311390200;
RA Jenkins J., Shevchik V.E., Hugouvieux-Cotte-Pattat N., Pickersgill R.W.;
RT "The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.";
RL J. Biol. Chem. 279:9139-9145(2004).
CC -!- FUNCTION: Presents an endo-cleaving activity on polygalacturonate or
CC partially methylated pectin. Is effective in the maceration of plant
CC tissue, and has an important role in soft-rot disease. Is 280-fold less
CC active against polygalacturonate than the major pectate lyase PelB.
CC When assayed on polygalacturonate, PelL releases oligogalacturonates of
CC different sizes; upon prolonged incubation, PelL degrades the primary
CC products to unsaturated tetramer and pentamer in addition to
CC unsaturated dimer and trimer. When assayed on oligogalacturonates
CC (degrees of polymerization of 2 to 8), it preferentially forms
CC unsaturated tetramer, and displays the highest activity on the octamer.
CC {ECO:0000269|PubMed:10368144, ECO:0000269|PubMed:8577252}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Eliminative cleavage of (1->4)-alpha-D-galacturonan to give
CC oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at
CC their non-reducing ends.; EC=4.2.2.2;
CC Evidence={ECO:0000269|PubMed:10368144, ECO:0000269|PubMed:8577252};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:8577252};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is around 8.0. {ECO:0000269|PubMed:8577252};
CC -!- PATHWAY: Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-
CC gluconate from pectin: step 2/5.
CC -!- SUBCELLULAR LOCATION: Secreted.
CC -!- INDUCTION: By pectic catabolic products. Transcription of pelL is
CC affected by growth phase, temperature, iron starvation, osmolarity,
CC anaerobiosis, nitrogen starvation and catabolite repression. Regulation
CC of pelL transcription appears to be independent of the KdgR repressor,
CC but under the control of PecS. {ECO:0000269|PubMed:8577252}.
CC -!- DISRUPTION PHENOTYPE: The pelL mutant displays a reduced virulence on
CC potato tubers and Saintpaulia ionantha plants.
CC {ECO:0000269|PubMed:8577252}.
CC -!- SIMILARITY: Belongs to the polysaccharide lyase 9 family.
CC {ECO:0000305}.
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DR EMBL; X81136; CAA57041.1; -; Genomic_DNA.
DR EMBL; CP002038; ADM99100.1; -; Genomic_DNA.
DR PIR; S69796; S69796.
DR RefSeq; WP_013318539.1; NC_014500.1.
DR PDB; 1RU4; X-ray; 1.60 A; A=26-425.
DR PDBsum; 1RU4; -.
DR AlphaFoldDB; P0C1A7; -.
DR SMR; P0C1A7; -.
DR STRING; 198628.Dda3937_02794; -.
DR CAZy; PL9; Polysaccharide Lyase Family 9.
DR EnsemblBacteria; ADM99100; ADM99100; Dda3937_02794.
DR GeneID; 9734342; -.
DR KEGG; ddd:Dda3937_02794; -.
DR PATRIC; fig|198628.6.peg.2890; -.
DR eggNOG; COG4733; Bacteria.
DR HOGENOM; CLU_030634_2_0_6; -.
DR OMA; QFWSGSN; -.
DR OrthoDB; 1177619at2; -.
DR BioCyc; DDAD198628:DDA3937_RS13610-MON; -.
DR UniPathway; UPA00545; UER00824.
DR EvolutionaryTrace; P0C1A7; -.
DR Proteomes; UP000006859; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030570; F:pectate lyase activity; IDA:ASAP.
DR GO; GO:0045490; P:pectin catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.160.20.10; -; 1.
DR InterPro; IPR039448; Beta_helix.
DR InterPro; IPR006626; PbH1.
DR InterPro; IPR012334; Pectin_lyas_fold.
DR InterPro; IPR011050; Pectin_lyase_fold/virulence.
DR Pfam; PF13229; Beta_helix; 1.
DR SMART; SM00710; PbH1; 4.
DR SUPFAM; SSF51126; SSF51126; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Disulfide bond; Lyase; Metal-binding;
KW Reference proteome; Secreted; Signal; Virulence.
FT SIGNAL 1..25
FT /evidence="ECO:0000305"
FT CHAIN 26..425
FT /note="Pectate lyase L"
FT /id="PRO_0000233032"
FT ACT_SITE 273
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:14670977"
FT BINDING 209
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 233
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 234
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 237
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 402
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 413
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 416
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 418
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT BINDING 423
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14670977,
FT ECO:0007744|PDB:1RU4"
FT DISULFID 28..114
FT /evidence="ECO:0000269|PubMed:14670977"
FT MUTAGEN 273
FT /note="K->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:14670977"
FT TURN 32..35
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 41..44
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:1RU4"
FT HELIX 63..69
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 107..111
FT /evidence="ECO:0007829|PDB:1RU4"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 134..137
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 142..151
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 170..173
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:1RU4"
FT TURN 201..205
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 251..254
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 284..287
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 289..292
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 294..299
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 313..323
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 333..337
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 339..343
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 349..355
FT /evidence="ECO:0007829|PDB:1RU4"
FT TURN 356..359
FT /evidence="ECO:0007829|PDB:1RU4"
FT HELIX 365..367
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 368..370
FT /evidence="ECO:0007829|PDB:1RU4"
FT HELIX 373..377
FT /evidence="ECO:0007829|PDB:1RU4"
FT TURN 399..402
FT /evidence="ECO:0007829|PDB:1RU4"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:1RU4"
SQ SEQUENCE 425 AA; 45484 MW; 8EAC71409FD53A6D CRC64;
MKYLNCFIST GLAAFFLVNS TSVLAADCSS DLTSGISTKR IYYVAPNGNS SNNGSSFNAP
MSFSAAMAAV NPGELILLKP GTYTIPYTQG KGNTITFNKS GKDGAPIYVA AANCGRAVFD
FSFPDSQWVQ ASYGFYVTGD YWYFKGVEVT RAGYQGAYVI GSHNTFENTA FHHNRNTGLE
INNGGSYNTV INSDAYRNYD PKKNGSMADG FGPKQKQGPG NRFVGCRAWE NSDDGFDLFD
SPQKVVIENS WAFRNGINYW NDSAFAGNGN GFKLGGNQAV GNHRITRSVA FGNVSKGFDQ
NNNAGGVTVI NNTSYKNGIN YGFGSNVQSG QKHYFRNNVS LSASVTVSNA DAKSNSWDTG
PAASASDFVS LDTSLATVSR DNDGTLPETS LFRLSANSKL INAGTKESNI SYSGSAPDLG
AFERN
