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Protein

Pectate lyase A

Gene

pelA

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+Note: Binds 1 Ca2+ ion per subunit.

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi174 – 1741CalciumBy similarity
Metal bindingi176 – 1761CalciumBy similarity
Metal bindingi216 – 2161CalciumBy similarity
Metal bindingi220 – 2201CalciumBy similarity
Active sitei273 – 2731Sequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

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 A (EC:4.2.2.2)
Gene namesi
Name:pelA
OrganismiDickeya chrysanthemi (Pectobacterium chrysanthemi) (Erwinia chrysanthemi)
Taxonomic identifieri556 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeDickeya

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3232Sequence analysisAdd
BLAST
Chaini33 – 393361Pectate lyase APRO_0000024852Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi330 ↔ 358

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1
393
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni38 – 414Combined sources
Beta strandi46 – 483Combined sources
Helixi49 – 513Combined sources
Beta strandi52 – 543Combined sources
Turni58 – 614Combined sources
Helixi64 – 663Combined sources
Beta strandi67 – 704Combined sources
Helixi73 – 808Combined sources
Turni81 – 844Combined sources
Beta strandi87 – 915Combined sources
Beta strandi93 – 964Combined sources
Turni97 – 1004Combined sources
Helixi106 – 1127Combined sources
Beta strandi113 – 1164Combined sources
Beta strandi119 – 1257Combined sources
Beta strandi131 – 14010Combined sources
Helixi141 – 1433Combined sources
Beta strandi146 – 1527Combined sources
Beta strandi154 – 1563Combined sources
Beta strandi164 – 1663Combined sources
Turni167 – 1693Combined sources
Beta strandi170 – 1723Combined sources
Beta strandi177 – 1815Combined sources
Beta strandi185 – 1917Combined sources
Beta strandi193 – 1953Combined sources
Helixi201 – 2033Combined sources
Beta strandi205 – 2073Combined sources
Beta strandi210 – 2123Combined sources
Beta strandi218 – 2214Combined sources
Beta strandi226 – 2327Combined sources
Beta strandi234 – 2407Combined sources
Beta strandi242 – 2454Combined sources
Helixi251 – 2544Combined sources
Beta strandi259 – 2646Combined sources
Beta strandi266 – 2727Combined sources
Beta strandi274 – 2796Combined sources
Beta strandi281 – 2866Combined sources
Beta strandi288 – 2925Combined sources
Beta strandi296 – 2983Combined sources
Beta strandi303 – 3064Combined sources
Beta strandi311 – 3166Combined sources
Beta strandi318 – 3225Combined sources
Helixi326 – 3327Combined sources
Beta strandi333 – 3375Combined sources
Beta strandi340 – 3456Combined sources
Beta strandi356 – 3594Combined sources
Helixi378 – 38710Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JRGX-ray2.10A/B33-393[»]
1JTAX-ray1.80A33-393[»]
1OOCX-ray2.94A/B33-393[»]
1PE9X-ray1.60A/B33-393[»]
ProteinModelPortaliP0C1A2.
SMRiP0C1A2. Positions 33-393.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C1A2.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Repeat, 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.

P0C1A2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMNKASGRSF TRSSKYLLAT LIAGMMASGV SAAELVSDKA LESAPTVGWA
60 70 80 90 100
SQNGFTTGGA AATSDNIYIV TNISEFTSAL SAGAEAKIIQ IKGTIDISGG
110 120 130 140 150
TPYTDFADQK ARSQINIPAN TTVIGLGTDA KFINGSLIID GTDGTNNVII
160 170 180 190 200
RNVYIQTPID VEPHYEKGDG WNAEWDAMNI TNGAHHVWID HVTISDGNFT
210 220 230 240 250
DDMYTTKDGE TYVQHDGALD IKRGSDYVTI SNSLIDQHDK TMLIGHNDTN
260 270 280 290 300
SAQDKGKLHV TLFNNVFNRV TERAPRVRYG SIHSFNNVFK GDAKDPVYRY
310 320 330 340 350
QYSFGIGTSG SVLSEGNSFT IANLSASKAC KVVKKFNGSI FSDNGSVLNG
360 370 380 390
SAVDLSGCGF SAYTSKIPYI YDVQPMTTEL AQSITDNAGS GKL
Length:393
Mass (Da):42,080
Last modified:April 18, 2006 - v1
Checksum:i20025C904FD7B345
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14509 Genomic DNA. Translation: AAA24843.1.
PIRiB31091. WZWC6A.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14509 Genomic DNA. Translation: AAA24843.1.
PIRiB31091. WZWC6A.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JRGX-ray2.10A/B33-393[»]
1JTAX-ray1.80A33-393[»]
1OOCX-ray2.94A/B33-393[»]
1PE9X-ray1.60A/B33-393[»]
ProteinModelPortaliP0C1A2.
SMRiP0C1A2. Positions 33-393.
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

EvolutionaryTraceiP0C1A2.

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...

Publicationsi

  1. "Structure and organization of the pel genes from Erwinia chrysanthemi EC16."
    Tamaki S.J., Gold S., Robeson M., Manulis S., Keen N.T.
    J. Bacteriol. 170:3468-3478(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: EC16.
  2. "Structure of pectate lyase A: comparison to other isoforms."
    Thomas L.M., Doan C.N., Oliver R.L., Yoder M.D.
    Acta Crystallogr. D 58:1008-1015(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 33-393.

Entry informationi

Entry nameiPLYA_DICCH
AccessioniPrimary (citable) accession number: P0C1A2
Secondary accession number(s): P29155
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: April 18, 2006
Last modified: October 14, 2015
This is version 44 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.