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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)DescriptionActionsGraphical viewLength
Binding sitei109Substrate1
Binding sitei153Substrate1
Sitei177Transition state stabilizer1
Active sitei178Proton donor1
Active sitei199Nucleophile1
Binding sitei219Substrate1
Binding sitei226Substrate1
Binding sitei230Substrate1
Binding sitei267Substrate1
Binding sitei269Substrate1
Binding sitei272Substrate; via amide nitrogen and carbonyl oxygen1

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

BioCyciMetaCyc: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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaeDickeya
Proteomesi
  • UP000006859 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi153Q → A: Strong decrease in affinity for substrate. 1 Publication1
Mutagenesisi177Q → A: Strong decrease in catalytic activity. 1 Publication1
Mutagenesisi178D → A: Loss of activity. 1 Publication1
Mutagenesisi198V → A: Strong decrease in catalytic activity. 1 Publication1
Mutagenesisi199D → A: Loss of activity. 1 Publication1
Mutagenesisi267R → A: Loss of activity. 1 Publication1
Mutagenesisi269W → A: Loss of activity. 1 Publication1
Mutagenesisi272T → A: Decreases affinity for substrate. 1 Publication1
Mutagenesisi306M → A: Strong decrease in catalytic activity. Decreases affinity for substrate. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24By similarityAdd BLAST24
ChainiPRO_000023303325 – 366Pectinesterase AAdd BLAST342

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi192 ↔ 2121 Publication

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi198628.Dda3937_03374.

Structurei

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi29 – 32Combined sources4
Beta strandi36 – 38Combined sources3
Beta strandi42 – 44Combined sources3
Helixi45 – 50Combined sources6
Beta strandi54 – 57Combined sources4
Beta strandi59 – 63Combined sources5
Beta strandi65 – 69Combined sources5
Beta strandi72 – 74Combined sources3
Beta strandi79 – 84Combined sources6
Turni86 – 88Combined sources3
Beta strandi89 – 93Combined sources5
Helixi108 – 111Combined sources4
Beta strandi114 – 117Combined sources4
Beta strandi119 – 121Combined sources3
Beta strandi123 – 131Combined sources9
Helixi135 – 140Combined sources6
Beta strandi156 – 159Combined sources4
Beta strandi164 – 174Combined sources11
Beta strandi180 – 182Combined sources3
Beta strandi184 – 191Combined sources8
Beta strandi193 – 211Combined sources19
Beta strandi213 – 216Combined sources4
Beta strandi229 – 234Combined sources6
Beta strandi244 – 248Combined sources5
Beta strandi250 – 255Combined sources6
Beta strandi263 – 266Combined sources4
Beta strandi272 – 275Combined sources4
Beta strandi278 – 281Combined sources4
Beta strandi288 – 293Combined sources6
Beta strandi300 – 302Combined sources3
Beta strandi306 – 309Combined sources4
Beta strandi315 – 318Combined sources4
Helixi320 – 322Combined sources3
Beta strandi323 – 329Combined sources7
Helixi346 – 349Combined sources4
Helixi350 – 352Combined sources3
Helixi354 – 358Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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
PDB 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.
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.
BioCyciMetaCyc: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: November 2, 2016
This is version 60 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.