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UniProtKB - P0C1A9 (PMEA_DICD3)

>sp|P0C1A9|PMEA_DICD3 Pectinesterase A OS=Dickeya dadantii (strain 3937) OX=198628 GN=pemA PE=1 SV=1
MLKTISGTLALSLIIAASVHQAQAATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFV
ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAK
DFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTL
YVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQ
KYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI
YGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGD
WTPTLP

Entry version 81 (25 May 2022)
Sequence version 1 (18 Apr 2006)
Previous versions | rss

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Protein

Pectinesterase A

Gene

pemA

Organism

Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937))

Status

Reviewed-Annotation score: -Experimental evidence at protein levelⁱ

Functionⁱ

Catalyzes the first step in maceration and soft-rotting of plant tissue.

2 Publications

Catalytic activityⁱ

[(1→4)-α-D-galacturonosyl methyl ester]_(n)
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Search chemical reactions in Rhea for this molecule.
+ n
H₂O
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
=
[(1→4)-α-D-galacturonosyl]_(n)
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
+ n
H⁺
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+ n
methanol
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
2 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "Characterization and overexpression of the pem gene encoding pectin methylesterase of Erwinia chrysanthemi strain 3937."
  Laurent F., Kotoujansky A., Labesse G., Bertheau Y.
  Gene 131:17-25(1993) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 25-34, FUNCTION, CATALYTIC ACTIVITY, PROBABLE PATHWAY, SUBUNIT, SUBCELLULAR LOCATION.
- Ref.4
  "Molecular basis of the activity of the phytopathogen pectin methylesterase."
  Fries M., Ihrig J., Brocklehurst K., Shevchik V.E., Pickersgill R.W.
  EMBO J. 26:3879-3887(2007) [PubMed] [Europe PMC] [Abstract]
  Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 25-366 IN COMPLEXES WITH SUBSTRATES AND PRODUCT, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, REACTION MECHANISM, PROBABLE PATHWAY, SUBUNIT, DISULFIDE BOND, MUTAGENESIS OF GLN-153; GLN-177; ASP-178; VAL-198; ASP-199; ARG-267; TRP-269; THR-272 AND MET-306.
EC:
3.1.1.11
- Search proteins in UniProtKB for this EC number.
- See the description of this EC number in ENZYME.
- Search reactions for this EC number in Rhea.
2 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "Characterization and overexpression of the pem gene encoding pectin methylesterase of Erwinia chrysanthemi strain 3937."
  Laurent F., Kotoujansky A., Labesse G., Bertheau Y.
  Gene 131:17-25(1993) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 25-34, FUNCTION, CATALYTIC ACTIVITY, PROBABLE PATHWAY, SUBUNIT, SUBCELLULAR LOCATION.
- Ref.4
  "Molecular basis of the activity of the phytopathogen pectin methylesterase."
  Fries M., Ihrig J., Brocklehurst K., Shevchik V.E., Pickersgill R.W.
  EMBO J. 26:3879-3887(2007) [PubMed] [Europe PMC] [Abstract]
  Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 25-366 IN COMPLEXES WITH SUBSTRATES AND PRODUCT, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, REACTION MECHANISM, PROBABLE PATHWAY, SUBUNIT, DISULFIDE BOND, MUTAGENESIS OF GLN-153; GLN-177; ASP-178; VAL-198; ASP-199; ARG-267; TRP-269; THR-272 AND MET-306.
Source:
Rhea
Search for this reaction in UniProtKB.
See the description of this reaction in Rhea.
. Show »« Hide
[(1→4)-α-D-galacturonosyl methyl ester]_(n)
zoom
+
n
H₂O
=
[(1→4)-α-D-galacturonosyl]_(n)
zoom
+
n
H⁺
+
n
methanol
zoom

Pathwayⁱ: pectin degradation

This protein is involved in step 1 of the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin.2 Publications 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 key	Position(s)	DescriptionActions	Length
Binding siteⁱ	109	Substrate1 Publication	1
Binding siteⁱ	153	Substrate1 Publication	1
Siteⁱ	177	Transition state stabilizer1 Publication	1
Active siteⁱ	178	Proton donor1 Publication	1
Active siteⁱ	199	Nucleophile1 Publication	1
Binding siteⁱ	219	Substrate1 Publication	1
Binding siteⁱ	226	Substrate1 Publication	1
Binding siteⁱ	230	Substrate1 Publication	1
Binding siteⁱ	267	Substrate1 Publication	1
Binding siteⁱ	269	Substrate1 Publication	1
Binding siteⁱ	272	Substrate; via amide nitrogen and carbonyl oxygen1 Publication	1

GO - Molecular functionⁱ

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

cell wall modification Source: InterPro
pectin catabolic process Source: UniProtKB-UniPathway

Complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Aspartyl esterase, Hydrolase
Biological process	Cell wall biogenesis/degradation

Enzyme and pathway databases

BioCycⁱ	DDAD198628:DDA3937_RS15630-MONOMER
UniPathwayⁱ	UPA00545;UER00823

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Pectinesterase A (EC:3.1.1.111 Publication) Short name: PE A Alternative name(s): Pectin methylesterase A Short name: PME1 Publication
Gene namesⁱ	Name:pemA1 Publication Synonyms:pem1 Publication Ordered Locus Names:Dda3937_03374
Organismⁱ	Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937))
Taxonomic identifierⁱ	198628 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Pectobacteriaceae › Dickeya › Dickeya dadantii
Proteomesⁱ	UP000006859 Componentⁱ: Chromosome

Keywords - Cellular componentⁱ

Secreted

Pathology & Biotechⁱ

Disruption phenotypeⁱ

Decreased growth on methylated oligogalacturides; double pemA-pemB deletions grow very poorly on methylated oligogalacturides.1 Publication

Mutagenesis

Feature key	Position(s)	DescriptionActions	Length
Mutagenesisⁱ	153	Q → A: Strong decrease in affinity for substrate. 1 Publication	1
Mutagenesisⁱ	177	Q → A: Strong decrease in catalytic activity. 1 Publication	1
Mutagenesisⁱ	178	D → A: Loss of activity. 1 Publication	1
Mutagenesisⁱ	198	V → A: Strong decrease in catalytic activity. 1 Publication	1
Mutagenesisⁱ	199	D → A: Loss of activity. 1 Publication	1
Mutagenesisⁱ	267	R → A: Loss of activity. 1 Publication	1
Mutagenesisⁱ	269	W → A: Loss of activity. 1 Publication	1
Mutagenesisⁱ	272	T → A: Decreases affinity for substrate. 1 Publication	1
Mutagenesisⁱ	306	M → A: Strong decrease in catalytic activity. Decreases affinity for substrate. 1 Publication	1

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Signal peptideⁱ	1 – 24	1 PublicationAdd BLAST		24
ChainⁱPRO_0000233033	25 – 366	Pectinesterase AAdd BLAST		342

Amino acid modifications

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Disulfide bondⁱ	192 ↔ 212	1 Publication

Keywords - PTMⁱ

Disulfide bond

Interactionⁱ

Subunit structureⁱ

Monomer.

2 Publications

Protein-protein interaction databases

STRINGⁱ	198628.Dda3937_03374

STRINGⁱ

198628.Dda3937_03374

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Beta strandⁱ	29 – 32	Combined sources	4
Beta strandⁱ	36 – 38	Combined sources	3
Beta strandⁱ	42 – 44	Combined sources	3
Helixⁱ	45 – 50	Combined sources	6
Beta strandⁱ	54 – 57	Combined sources	4
Beta strandⁱ	59 – 63	Combined sources	5
Beta strandⁱ	65 – 69	Combined sources	5
Beta strandⁱ	72 – 74	Combined sources	3
Beta strandⁱ	79 – 84	Combined sources	6
Turnⁱ	86 – 88	Combined sources	3
Beta strandⁱ	89 – 93	Combined sources	5
Helixⁱ	108 – 111	Combined sources	4
Beta strandⁱ	114 – 117	Combined sources	4
Beta strandⁱ	119 – 121	Combined sources	3
Beta strandⁱ	123 – 131	Combined sources	9
Helixⁱ	135 – 140	Combined sources	6
Beta strandⁱ	156 – 159	Combined sources	4
Beta strandⁱ	164 – 174	Combined sources	11
Beta strandⁱ	180 – 182	Combined sources	3
Beta strandⁱ	184 – 191	Combined sources	8
Beta strandⁱ	193 – 211	Combined sources	19
Beta strandⁱ	213 – 216	Combined sources	4
Beta strandⁱ	229 – 234	Combined sources	6
Beta strandⁱ	244 – 248	Combined sources	5
Beta strandⁱ	250 – 255	Combined sources	6
Beta strandⁱ	263 – 266	Combined sources	4
Beta strandⁱ	272 – 275	Combined sources	4
Beta strandⁱ	278 – 281	Combined sources	4
Beta strandⁱ	288 – 293	Combined sources	6
Beta strandⁱ	300 – 302	Combined sources	3
Beta strandⁱ	306 – 309	Combined sources	4
Beta strandⁱ	315 – 318	Combined sources	4
Helixⁱ	320 – 322	Combined sources	3
Beta strandⁱ	323 – 329	Combined sources	7
Helixⁱ	346 – 349	Combined sources	4
Helixⁱ	350 – 352	Combined sources	3
Helixⁱ	354 – 358	Combined sources	5

Show more details

3D structure databases

AlphaFoldDBⁱ	P0C1A9
SMRⁱ	P0C1A9
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Miscellaneous databases

EvolutionaryTraceⁱ	P0C1A9

EvolutionaryTraceⁱ

P0C1A9

Family & Domainsⁱ

Sequence similaritiesⁱ

Belongs to the pectinesterase family.Curated

Keywords - Domainⁱ

Signal

Phylogenomic databases

eggNOGⁱ	COG4677, Bacteria
HOGENOMⁱ	CLU_012243_3_1_6
OMAⁱ	NRVAWCR
Database of Orthologous Groups More...OrthoDBⁱ	1095798at2

Family and domain databases

Gene3Dⁱ	2.160.20.10, 1 hit
InterProⁱ	View protein in InterPro IPR012334, Pectin_lyas_fold IPR011050, Pectin_lyase_fold/virulence IPR033131, Pectinesterase_Asp_AS IPR000070, Pectinesterase_cat
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF01095, Pectinesterase, 1 hit
SUPFAMⁱ	SSF51126, SSF51126, 1 hit
PROSITEⁱ	View protein in PROSITE PS00503, PECTINESTERASE_2, 1 hit

Sequenceⁱ

Sequence statusⁱ: Complete.

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

P0C1A9-1 [UniParc]FASTA Add to basket

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        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

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	L07644 Genomic DNA Translation: AAA24852.1 CP002038 Genomic DNA Translation: ADM99554.1
PIRⁱ	JN0799
NCBI Reference Sequences More...RefSeqⁱ	WP_013318985.1, NC_014500.1

Genome annotation databases

EnsemblBacteriaⁱ	ADM99554; ADM99554; Dda3937_03374
GeneIDⁱ	9734805
KEGGⁱ	ddd:Dda3937_03374
PATRICⁱ	fig\|198628.6.peg.3312

Similar proteinsⁱ

90% Identity
50% Identity

Protein	Similar proteins		Species	Score	Length	Source
P0C1A9	Pectinesterase A	)	DICCH		366	UniRef90_P0C1A9
Pectinesterase		Dickeya sp. DCE-01		368
Pectinesterase (Fragment)		DICDA		366
Pectinesterase		DICC1		366
Pectinesterase		Dickeya sp. ws52		366
+34

Protein	Similar proteins		Species	Score	Length	Source
P0C1A9	Pectinesterase A	)	DICCH		366	UniRef50_P0C1A9
Pectinesterase		Dickeya sp. DCE-01		368
Pectinesterase (Fragment)		DICDA		366
Pectinesterase		Dickeya undicola		366
Pectinesterase		Dickeya fangzhongdai		366
+376

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
PIRⁱ	JN0799
RefSeqⁱ	WP_013318985.1, NC_014500.1

3D structure databases

Select the link destinations: Protein Data Bank Europe More...PDBeⁱ Protein Data Bank RCSB More...RCSB PDBⁱ Protein Data Bank Japan More...PDBjⁱ Links Updated	PDB entry	Method	Resolution (Å)	Chain	Positions	PDBsum
	2NSP	X-ray	1.70	A/B	25-366	[»]
	2NST	X-ray	1.70	A/B	25-366	[»]
	2NT6	X-ray	1.70	A/B	25-366	[»]
	2NT9	X-ray	1.90	A/B	25-366	[»]
	2NTB	X-ray	1.80	A/B	25-366	[»]
	2NTP	X-ray	1.70	A/B	25-366	[»]
	2NTQ	X-ray	1.80	A/B	25-366	[»]
AlphaFoldDBⁱ	P0C1A9
SMRⁱ	P0C1A9
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Protein-protein interaction databases

STRINGⁱ	198628.Dda3937_03374

STRINGⁱ

198628.Dda3937_03374

Genome annotation databases

EnsemblBacteriaⁱ	ADM99554; ADM99554; Dda3937_03374
GeneIDⁱ	9734805
KEGGⁱ	ddd:Dda3937_03374
PATRICⁱ	fig\|198628.6.peg.3312

Phylogenomic databases

eggNOGⁱ	COG4677, Bacteria
HOGENOMⁱ	CLU_012243_3_1_6
OMAⁱ	NRVAWCR
OrthoDBⁱ	1095798at2

Enzyme and pathway databases

UniPathwayⁱ	UPA00545;UER00823
BioCycⁱ	DDAD198628:DDA3937_RS15630-MONOMER

Miscellaneous databases

EvolutionaryTraceⁱ	P0C1A9

EvolutionaryTraceⁱ

P0C1A9

Family and domain databases

Gene3Dⁱ	2.160.20.10, 1 hit
InterProⁱ	View protein in InterPro IPR012334, Pectin_lyas_fold IPR011050, Pectin_lyase_fold/virulence IPR033131, Pectinesterase_Asp_AS IPR000070, Pectinesterase_cat
Pfamⁱ	View protein in Pfam PF01095, Pectinesterase, 1 hit
SUPFAMⁱ	SSF51126, SSF51126, 1 hit
PROSITEⁱ	View protein in PROSITE PS00503, PECTINESTERASE_2, 1 hit
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	PMEA_DICD3
Accessionⁱ	P0C1A9Primary (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:	May 25, 2022
	This is version 81 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Prokaryotic Protein Annotation Program

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UniParc

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Annotation systems

Supporting data

UniProtKB - P0C1A9 (PMEA_DICD3)

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Pectinesterase A

pemA

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: pectin degradation

Sites

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted

Extracellular region or secreted

Keywords - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Amino acid modifications

Keywords - PTMi

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

3D structure databases

Miscellaneous databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

Phylogenomic databases

Family and domain databases

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Miscellaneous databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Documents

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Functionⁱ

Catalytic activityⁱ

Pathwayⁱ: pectin degradation

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Keywords - PTMⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Keywords - Domainⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ