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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)DescriptionActionsGraphical viewLength
Metal bindingi209Calcium 11
Metal bindingi233Calcium 11
Metal bindingi234Calcium 11
Metal bindingi237Calcium 11
Active sitei273Proton acceptor1 Publication1
Metal bindingi402Calcium 21
Metal bindingi413Calcium 2; via carbonyl oxygen1
Metal bindingi416Calcium 2; via carbonyl oxygen1
Metal bindingi418Calcium 21
Metal bindingi423Calcium 21

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

UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL9. Polysaccharide Lyase Family 9.

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaeDickeya
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)DescriptionActionsGraphical viewLength
Mutagenesisi273K → A: Loss of catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 25CuratedAdd BLAST25
ChainiPRO_000023303226 – 425Pectate lyase LAdd BLAST400

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
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

1425
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni32 – 35Combined sources4
Beta strandi41 – 44Combined sources4
Beta strandi54 – 56Combined sources3
Helixi63 – 69Combined sources7
Beta strandi75 – 78Combined sources4
Beta strandi80 – 84Combined sources5
Beta strandi95 – 97Combined sources3
Beta strandi107 – 111Combined sources5
Helixi112 – 114Combined sources3
Beta strandi117 – 120Combined sources4
Beta strandi134 – 137Combined sources4
Beta strandi142 – 151Combined sources10
Beta strandi156 – 159Combined sources4
Beta strandi161 – 163Combined sources3
Beta strandi165 – 168Combined sources4
Beta strandi170 – 173Combined sources4
Beta strandi178 – 181Combined sources4
Beta strandi189 – 192Combined sources4
Beta strandi194 – 196Combined sources3
Turni201 – 205Combined sources5
Beta strandi210 – 213Combined sources4
Beta strandi222 – 225Combined sources4
Beta strandi227 – 230Combined sources4
Beta strandi235 – 237Combined sources3
Beta strandi246 – 249Combined sources4
Beta strandi251 – 254Combined sources4
Beta strandi271 – 273Combined sources3
Beta strandi284 – 287Combined sources4
Beta strandi289 – 292Combined sources4
Beta strandi294 – 299Combined sources6
Beta strandi308 – 311Combined sources4
Beta strandi313 – 323Combined sources11
Beta strandi333 – 337Combined sources5
Beta strandi339 – 343Combined sources5
Beta strandi345 – 347Combined sources3
Beta strandi349 – 355Combined sources7
Turni356 – 359Combined sources4
Helixi365 – 367Combined sources3
Beta strandi368 – 370Combined sources3
Helixi373 – 377Combined sources5
Turni399 – 402Combined sources4
Beta strandi419 – 421Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RU4X-ray1.60A26-425[»]
ProteinModelPortaliP0C1A7.
SMRiP0C1A7.
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.
OrthoDBiPOG091H0FJA.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RU4X-ray1.60A26-425[»]
ProteinModelPortaliP0C1A7.
SMRiP0C1A7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198628.Dda3937_02794.

Protein family/group databases

CAZyiPL9. Polysaccharide Lyase Family 9.

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.
OrthoDBiPOG091H0FJA.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.

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...

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 2, 2016
This is version 56 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.