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Protein

Pectate lyase C

Gene

pelC

Organism
Dickeya chrysanthemi (Pectobacterium chrysanthemi) (Erwinia chrysanthemi)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in maceration and soft-rotting of plant tissue.

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.

Cofactori

Ca2+1 PublicationNote: Binds 1 Ca2+ ion per subunit.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 (NM75_02575), Pectinesterase A (pemA), Pectinesterase (NM75_10885)
  2. Pectate lyase C (pelC), Pectate lyase D (pelD), Pectate lyase L (pelL), Pectate lyase E (pelE), Pectate lyase A (pelA), Pectate lyase B (pelB), Pectate lyase E (pelE)
  3. no protein annotated in this organism
  4. 5-dehydro-4-deoxy-D-glucuronate isomerase (NM75_18995), 5-dehydro-4-deoxy-D-glucuronate isomerase (NM75_20295)
  5. no protein annotated in this organism
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 bindingi151Calcium1 Publication1
Metal bindingi153Calcium1 Publication1
Metal bindingi188Calcium1 Publication1
Metal bindingi192Calcium1 Publication1
Active sitei240Sequence analysis1

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

BRENDAi4.2.2.2. 2141.
UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectate lyase C (EC:4.2.2.2)
Gene namesi
Name:pelC1 Publication
OrganismiDickeya chrysanthemi (Pectobacterium chrysanthemi) (Erwinia chrysanthemi)
Taxonomic identifieri556 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaeDickeya

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 22Add BLAST22
ChainiPRO_000002485423 – 375Pectate lyase CAdd BLAST353

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi94 ↔ 177
Disulfide bondi351 ↔ 374

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1375
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi27 – 29Combined sources3
Beta strandi41 – 47Combined sources7
Helixi48 – 57Combined sources10
Beta strandi74 – 78Combined sources5
Helixi83 – 90Combined sources8
Helixi93 – 95Combined sources3
Turni96 – 98Combined sources3
Beta strandi103 – 109Combined sources7
Beta strandi113 – 117Combined sources5
Beta strandi123 – 131Combined sources9
Beta strandi134 – 139Combined sources6
Beta strandi141 – 144Combined sources4
Helixi148 – 150Combined sources3
Beta strandi154 – 159Combined sources6
Beta strandi162 – 167Combined sources6
Beta strandi169 – 171Combined sources3
Helixi181 – 183Combined sources3
Beta strandi190 – 196Combined sources7
Beta strandi199 – 204Combined sources6
Beta strandi206 – 212Combined sources7
Beta strandi215 – 219Combined sources5
Beta strandi226 – 231Combined sources6
Beta strandi233 – 239Combined sources7
Beta strandi243 – 253Combined sources11
Beta strandi255 – 261Combined sources7
Beta strandi263 – 267Combined sources5
Beta strandi271 – 276Combined sources6
Beta strandi278 – 288Combined sources11
Beta strandi290 – 294Combined sources5
Beta strandi297 – 302Combined sources6
Helixi310 – 314Combined sources5
Helixi349 – 355Combined sources7
Helixi356 – 358Combined sources3
Beta strandi360 – 364Combined sources5
Helixi371 – 373Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AIRX-ray2.20A23-375[»]
1O88X-ray2.20A23-375[»]
1O8DX-ray2.20A23-375[»]
1O8EX-ray2.20A23-375[»]
1O8FX-ray2.20A23-375[»]
1O8GX-ray2.20A23-375[»]
1O8HX-ray2.20A23-375[»]
1O8IX-ray2.20A23-375[»]
1O8JX-ray2.20A23-375[»]
1O8KX-ray2.20A23-375[»]
1O8LX-ray2.20A23-375[»]
1O8MX-ray2.20A23-375[»]
1PLUX-ray2.20A23-375[»]
2EWEX-ray2.20A23-375[»]
2PECX-ray2.20A23-375[»]
ProteinModelPortaliP11073.
SMRiP11073.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11073.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR002022. Amb_allergen_dom.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00544. Pec_lyase_C. 1 hit.
[Graphical view]
SMARTiSM00656. Amb_all. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P11073-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKSLITPITA GLLLALSQPL LAATDTGGYA ATAGGNVTGA VSKTATSMQD
60 70 80 90 100
IVNIIDAARL DANGKKVKGG AYPLVITYTG NEDSLINAAA ANICGQWSKD
110 120 130 140 150
PRGVEIKEFT KGITIIGANG SSANFGIWIK KSSDVVVQNM RIGYLPGGAK
160 170 180 190 200
DGDMIRVDDS PNVWVDHNEL FAANHECDGT PDNDTTFESA VDIKGASNTV
210 220 230 240 250
TVSYNYIHGV KKVGLDGSSS SDTGRNITYH HNYYNDVNAR LPLQRGGLVH
260 270 280 290 300
AYNNLYTNIT GSGLNVRQNG QALIENNWFE KAINPVTSRY DGKNFGTWVL
310 320 330 340 350
KGNNITKPAD FSTYSITWTA DTKPYVNADS WTSTGTFPTV AYNYSPVSAQ
360 370
CVKDKLPGYA GVGKNLATLT STACK
Length:375
Mass (Da):39,944
Last modified:July 1, 1989 - v1
Checksum:iF76DD8195A35B886
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19411 Genomic DNA. Translation: AAA24849.1.
PIRiA31091. WZWC6C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19411 Genomic DNA. Translation: AAA24849.1.
PIRiA31091. WZWC6C.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AIRX-ray2.20A23-375[»]
1O88X-ray2.20A23-375[»]
1O8DX-ray2.20A23-375[»]
1O8EX-ray2.20A23-375[»]
1O8FX-ray2.20A23-375[»]
1O8GX-ray2.20A23-375[»]
1O8HX-ray2.20A23-375[»]
1O8IX-ray2.20A23-375[»]
1O8JX-ray2.20A23-375[»]
1O8KX-ray2.20A23-375[»]
1O8LX-ray2.20A23-375[»]
1O8MX-ray2.20A23-375[»]
1PLUX-ray2.20A23-375[»]
2EWEX-ray2.20A23-375[»]
2PECX-ray2.20A23-375[»]
ProteinModelPortaliP11073.
SMRiP11073.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BRENDAi4.2.2.2. 2141.

Miscellaneous databases

EvolutionaryTraceiP11073.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR002022. Amb_allergen_dom.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00544. Pec_lyase_C. 1 hit.
[Graphical view]
SMARTiSM00656. Amb_all. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPLYC_DICCH
AccessioniPrimary (citable) accession number: P11073
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 108 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

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.