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Protein

Pectinesterase A

Gene

pemA

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

Involved in maceration and soft-rotting of plant tissue.

Catalytic activityi

Pectin + n H2O = n methanol + pectate.

Pathwayi: pectin degradation

This protein is involved in step 1 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
Binding sitei109 – 1091Substrate
Binding sitei153 – 1531Substrate
Sitei177 – 1771Transition state stabilizer
Active sitei178 – 1781Proton donor
Active sitei199 – 1991Nucleophile
Binding sitei219 – 2191Substrate
Binding sitei226 – 2261Substrate
Binding sitei230 – 2301Substrate
Binding sitei267 – 2671Substrate
Binding sitei269 – 2691Substrate
Binding sitei272 – 2721Substrate; via amide nitrogen and carbonyl oxygen

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl esterase, Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation

Enzyme and pathway databases

BioCyciDDAD198628:GHFQ-3420-MONOMER.
MetaCyc:MONOMER-15656.
UniPathwayiUPA00545; UER00823.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectinesterase A (EC:3.1.1.11)
Short name:
PE A
Alternative name(s):
Pectin methylesterase A
Gene namesi
Name:pemA
Synonyms:pem
Ordered Locus Names:Dda3937_03374
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

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi153 – 1531Q → A: Strong decrease in affinity for substrate. 1 Publication
Mutagenesisi177 – 1771Q → A: Strong decrease in catalytic activity. 1 Publication
Mutagenesisi178 – 1781D → A: Loss of activity. 1 Publication
Mutagenesisi198 – 1981V → A: Strong decrease in catalytic activity. 1 Publication
Mutagenesisi199 – 1991D → A: Loss of activity. 1 Publication
Mutagenesisi267 – 2671R → A: Loss of activity. 1 Publication
Mutagenesisi269 – 2691W → A: Loss of activity. 1 Publication
Mutagenesisi272 – 2721T → A: Decreases affinity for substrate. 1 Publication
Mutagenesisi306 – 3061M → A: Strong decrease in catalytic activity. Decreases affinity for substrate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424By similarityAdd
BLAST
Chaini25 – 366342Pectinesterase APRO_0000233033Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi192 ↔ 2121 Publication

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi198628.Dda3937_03374.

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi29 – 324Combined sources
Beta strandi36 – 383Combined sources
Beta strandi42 – 443Combined sources
Helixi45 – 506Combined sources
Beta strandi54 – 574Combined sources
Beta strandi59 – 635Combined sources
Beta strandi65 – 695Combined sources
Beta strandi72 – 743Combined sources
Beta strandi79 – 846Combined sources
Turni86 – 883Combined sources
Beta strandi89 – 935Combined sources
Helixi108 – 1114Combined sources
Beta strandi114 – 1174Combined sources
Beta strandi119 – 1213Combined sources
Beta strandi123 – 1319Combined sources
Helixi135 – 1406Combined sources
Beta strandi156 – 1594Combined sources
Beta strandi164 – 17411Combined sources
Beta strandi180 – 1823Combined sources
Beta strandi184 – 1918Combined sources
Beta strandi193 – 21119Combined sources
Beta strandi213 – 2164Combined sources
Beta strandi229 – 2346Combined sources
Beta strandi244 – 2485Combined sources
Beta strandi250 – 2556Combined sources
Beta strandi263 – 2664Combined sources
Beta strandi272 – 2754Combined sources
Beta strandi278 – 2814Combined sources
Beta strandi288 – 2936Combined sources
Beta strandi300 – 3023Combined sources
Beta strandi306 – 3094Combined sources
Beta strandi315 – 3184Combined sources
Helixi320 – 3223Combined sources
Beta strandi323 – 3297Combined sources
Helixi346 – 3494Combined sources
Helixi350 – 3523Combined sources
Helixi354 – 3585Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NSPX-ray1.70A/B25-366[»]
2NSTX-ray1.70A/B25-366[»]
2NT6X-ray1.70A/B25-366[»]
2NT9X-ray1.90A/B25-366[»]
2NTBX-ray1.80A/B25-366[»]
2NTPX-ray1.70A/B25-366[»]
2NTQX-ray1.80A/B25-366[»]
ProteinModelPortaliP0C1A9.
SMRiP0C1A9. Positions 25-366.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C1A9.

Family & Domainsi

Sequence similaritiesi

Belongs to the pectinesterase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105NBR. Bacteria.
COG4677. LUCA.
HOGENOMiHOG000217409.
KOiK01051.
OMAiFYEYKST.
OrthoDBiPOG091H0DD6.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
IPR033131. Pectinesterase_Asp_AS.
IPR000070. Pectinesterase_cat.
[Graphical view]
PfamiPF01095. Pectinesterase. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
PROSITEiPS00503. PECTINESTERASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0C1A9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKTISGTLA LSLIIAASVH QAQAATTYNA VVSKSSSDGK TFKTIADAIA
60 70 80 90 100
SAPAGSTPFV ILIKNGVYNE RLTITRNNLH LKGESRNGAV IAAATAAGTL
110 120 130 140 150
KSDGSKWGTA GSSTITISAK DFSAQSLTIR NDFDFPANQA KSDSDSSKIK
160 170 180 190 200
DTQAVALYVT KSGDRAYFKD VSLVGYQDTL YVSGGRSFFS DCRISGTVDF
210 220 230 240 250
IFGDGTALFN NCDLVSRYRA DVKSGNVSGY LTAPSTNINQ KYGLVITNSR
260 270 280 290 300
VIRESDSVPA KSYGLGRPWH PTTTFSDGRY ADPNAIGQTV FLNTSMDNHI
310 320 330 340 350
YGWDKMSGKD KNGNTIWFNP EDSRFFEYKS YGAGATVSKD RRQLTDAQAA
360
EYTQSKVLGD WTPTLP
Length:366
Mass (Da):39,373
Last modified:April 18, 2006 - v1
Checksum:iC67C1A4D2C04735F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07644 Genomic DNA. Translation: AAA24852.1.
CP002038 Genomic DNA. Translation: ADM99554.1.
PIRiJN0799.
RefSeqiWP_013318985.1. NC_014500.1.

Genome annotation databases

EnsemblBacteriaiADM99554; ADM99554; Dda3937_03374.
GeneIDi9734805.
KEGGiddd:Dda3937_03374.
PATRICi42318999. VBIDicDad25310_3312.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07644 Genomic DNA. Translation: AAA24852.1.
CP002038 Genomic DNA. Translation: ADM99554.1.
PIRiJN0799.
RefSeqiWP_013318985.1. NC_014500.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NSPX-ray1.70A/B25-366[»]
2NSTX-ray1.70A/B25-366[»]
2NT6X-ray1.70A/B25-366[»]
2NT9X-ray1.90A/B25-366[»]
2NTBX-ray1.80A/B25-366[»]
2NTPX-ray1.70A/B25-366[»]
2NTQX-ray1.80A/B25-366[»]
ProteinModelPortaliP0C1A9.
SMRiP0C1A9. Positions 25-366.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198628.Dda3937_03374.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADM99554; ADM99554; Dda3937_03374.
GeneIDi9734805.
KEGGiddd:Dda3937_03374.
PATRICi42318999. VBIDicDad25310_3312.

Phylogenomic databases

eggNOGiENOG4105NBR. Bacteria.
COG4677. LUCA.
HOGENOMiHOG000217409.
KOiK01051.
OMAiFYEYKST.
OrthoDBiPOG091H0DD6.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00823.
BioCyciDDAD198628:GHFQ-3420-MONOMER.
MetaCyc:MONOMER-15656.

Miscellaneous databases

EvolutionaryTraceiP0C1A9.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
IPR033131. Pectinesterase_Asp_AS.
IPR000070. Pectinesterase_cat.
[Graphical view]
PfamiPF01095. Pectinesterase. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
PROSITEiPS00503. PECTINESTERASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPMEA_DICD3
AccessioniPrimary (citable) accession number: P0C1A9
Secondary accession number(s): E0SAZ5, P07863
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: April 18, 2006
Last modified: September 7, 2016
This is version 58 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.