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Protein

Pectate lyase L

Gene

pelL

Organism
Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. Is effective in the maceration of plant tissue, and has an important role in soft-rot disease. Is 280-fold less active against polygalacturonate than the major pectate lyase PelB. When assayed on polygalacturonate, PelL releases oligogalacturonates of different sizes; upon prolonged incubation, PelL degrades the primary products to unsaturated tetramer and pentamer in addition to unsaturated dimer and trimer. When assayed on oligogalacturonates (degrees of polymerization of 2 to 8), it preferentially forms unsaturated tetramer, and displays the highest activity on the octamer.2 Publications

Catalytic activityi

Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.2 Publications

Cofactori

Ca2+1 Publication

pH dependencei

Optimum pH is around 8.0.1 Publication

Pathwayi: pectin degradation

This protein is involved in step 2 of the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Pectinesterase A (pemA), Pectinesterase B (pemB)
  2. Pectate lyase L (pelL), Pectate lyase E (pelE), Pectate lyase A (pelA)
  3. Oligogalacturonate lyase (ogl)
  4. 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (kduI)
  5. 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (kduD)
This subpathway is part of the pathway pectin degradation, which is itself part of Glycan metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin, the pathway pectin degradation and in Glycan metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi209 – 2091Calcium 1
Metal bindingi233 – 2331Calcium 1
Metal bindingi234 – 2341Calcium 1
Metal bindingi237 – 2371Calcium 1
Active sitei273 – 2731Proton acceptor1 Publication
Metal bindingi402 – 4021Calcium 2
Metal bindingi413 – 4131Calcium 2; via carbonyl oxygen
Metal bindingi416 – 4161Calcium 2; via carbonyl oxygen
Metal bindingi418 – 4181Calcium 2
Metal bindingi423 – 4231Calcium 2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Virulence

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciDDAD198628:GHFQ-2957-MONOMER.
UniPathwayiUPA00545; UER00824.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectate lyase L (EC:4.2.2.2)
Alternative name(s):
Pectate transeliminase
Pel9A
Gene namesi
Name:pelL
Ordered Locus Names:Dda3937_02794
OrganismiDickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937))
Taxonomic identifieri198628 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeDickeya
Proteomesi
  • UP000006859 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Disruption phenotypei

The pelL mutant displays a reduced virulence on potato tubers and Saintpaulia ionantha plants.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi273 – 2731K → A: Loss of catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2525CuratedAdd
BLAST
Chaini26 – 425400Pectate lyase LPRO_0000233032Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi28 ↔ 114

Keywords - PTMi

Disulfide bond

Expressioni

Inductioni

By pectic catabolic products. Transcription of pelL is affected by growth phase, temperature, iron starvation, osmolarity, anaerobiosis, nitrogen starvation and catabolite repression. Regulation of pelL transcription appears to be independent of the KdgR repressor, but under the control of PecS.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi198628.Dda3937_02794.

Structurei

Secondary structure

1
425
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni32 – 354Combined sources
Beta strandi41 – 444Combined sources
Beta strandi54 – 563Combined sources
Helixi63 – 697Combined sources
Beta strandi75 – 784Combined sources
Beta strandi80 – 845Combined sources
Beta strandi95 – 973Combined sources
Beta strandi107 – 1115Combined sources
Helixi112 – 1143Combined sources
Beta strandi117 – 1204Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi142 – 15110Combined sources
Beta strandi156 – 1594Combined sources
Beta strandi161 – 1633Combined sources
Beta strandi165 – 1684Combined sources
Beta strandi170 – 1734Combined sources
Beta strandi178 – 1814Combined sources
Beta strandi189 – 1924Combined sources
Beta strandi194 – 1963Combined sources
Turni201 – 2055Combined sources
Beta strandi210 – 2134Combined sources
Beta strandi222 – 2254Combined sources
Beta strandi227 – 2304Combined sources
Beta strandi235 – 2373Combined sources
Beta strandi246 – 2494Combined sources
Beta strandi251 – 2544Combined sources
Beta strandi271 – 2733Combined sources
Beta strandi284 – 2874Combined sources
Beta strandi289 – 2924Combined sources
Beta strandi294 – 2996Combined sources
Beta strandi308 – 3114Combined sources
Beta strandi313 – 32311Combined sources
Beta strandi333 – 3375Combined sources
Beta strandi339 – 3435Combined sources
Beta strandi345 – 3473Combined sources
Beta strandi349 – 3557Combined sources
Turni356 – 3594Combined sources
Helixi365 – 3673Combined sources
Beta strandi368 – 3703Combined sources
Helixi373 – 3775Combined sources
Turni399 – 4024Combined sources
Beta strandi419 – 4213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RU4X-ray1.60A26-425[»]
ProteinModelPortaliP0C1A7.
SMRiP0C1A7. Positions 26-425.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C1A7.

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 9 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4108J21. Bacteria.
ENOG410XT60. LUCA.
HOGENOMiHOG000217148.
OMAiENVETHH.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR006626. PbH1.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
SMARTiSM00710. PbH1. 4 hits.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0C1A7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKYLNCFIST GLAAFFLVNS TSVLAADCSS DLTSGISTKR IYYVAPNGNS
60 70 80 90 100
SNNGSSFNAP MSFSAAMAAV NPGELILLKP GTYTIPYTQG KGNTITFNKS
110 120 130 140 150
GKDGAPIYVA AANCGRAVFD FSFPDSQWVQ ASYGFYVTGD YWYFKGVEVT
160 170 180 190 200
RAGYQGAYVI GSHNTFENTA FHHNRNTGLE INNGGSYNTV INSDAYRNYD
210 220 230 240 250
PKKNGSMADG FGPKQKQGPG NRFVGCRAWE NSDDGFDLFD SPQKVVIENS
260 270 280 290 300
WAFRNGINYW NDSAFAGNGN GFKLGGNQAV GNHRITRSVA FGNVSKGFDQ
310 320 330 340 350
NNNAGGVTVI NNTSYKNGIN YGFGSNVQSG QKHYFRNNVS LSASVTVSNA
360 370 380 390 400
DAKSNSWDTG PAASASDFVS LDTSLATVSR DNDGTLPETS LFRLSANSKL
410 420
INAGTKESNI SYSGSAPDLG AFERN
Length:425
Mass (Da):45,484
Last modified:April 18, 2006 - v1
Checksum:i8EAC71409FD53A6D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X81136 Genomic DNA. Translation: CAA57041.1.
CP002038 Genomic DNA. Translation: ADM99100.1.
PIRiS69796.
RefSeqiWP_013318539.1. NC_014500.1.

Genome annotation databases

EnsemblBacteriaiADM99100; ADM99100; Dda3937_02794.
GeneIDi9734342.
KEGGiddd:Dda3937_02794.
PATRICi42318139. VBIDicDad25310_2890.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X81136 Genomic DNA. Translation: CAA57041.1.
CP002038 Genomic DNA. Translation: ADM99100.1.
PIRiS69796.
RefSeqiWP_013318539.1. NC_014500.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RU4X-ray1.60A26-425[»]
ProteinModelPortaliP0C1A7.
SMRiP0C1A7. Positions 26-425.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198628.Dda3937_02794.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADM99100; ADM99100; Dda3937_02794.
GeneIDi9734342.
KEGGiddd:Dda3937_02794.
PATRICi42318139. VBIDicDad25310_2890.

Phylogenomic databases

eggNOGiENOG4108J21. Bacteria.
ENOG410XT60. LUCA.
HOGENOMiHOG000217148.
OMAiENVETHH.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BioCyciDDAD198628:GHFQ-2957-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0C1A7.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR006626. PbH1.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
SMARTiSM00710. PbH1. 4 hits.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the pelL gene encoding a novel pectate lyase of Erwinia chrysanthemi 3937."
    Lojkowska E., Masclaux C., Boccara M., Robert-Baudouy J., Hugouvieux-Cotte-Pattat N.
    Mol. Microbiol. 16:1183-1195(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR, PH DEPENDENCE, INDUCTION, ROLE IN SOFT-ROT DISEASE, DISRUPTION PHENOTYPE.
    Strain: 3937.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 3937.
  3. "Crystallization and preliminary X-ray analysis of a member of a new family of pectate lyases, PelL from Erwinia chrysanthemi."
    Shevchik V., Scott M., Mayans O., Jenkins J.
    Acta Crystallogr. D 54:419-422(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
    Strain: 3937.
  4. "Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937."
    Roy C., Kester H., Visser J., Shevchik V., Hugouvieux-Cotte-Pattat N., Robert-Baudouy J., Benen J.
    J. Bacteriol. 181:3705-3709(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  5. "The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi."
    Jenkins J., Shevchik V.E., Hugouvieux-Cotte-Pattat N., Pickersgill R.W.
    J. Biol. Chem. 279:9139-9145(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 26-425 IN COMPLEX WITH CALCIUM IONS, ACTIVE SITE, CATALYTIC MECHANISM, MUTAGENESIS OF LYS-273.
    Strain: 3937.

Entry informationi

Entry nameiPLYL_DICD3
AccessioniPrimary (citable) accession number: P0C1A7
Secondary accession number(s): E0SIP1, Q47473, Q59421
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: April 18, 2006
Last modified: November 11, 2015
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.