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Protein

Pectinesterase/pectinesterase inhibitor 3

Gene

PME3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Acts in the modification of cell walls via demethylesterification of cell wall pectin.By similarity

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. Probable pectinesterase/pectinesterase inhibitor 7 (PME7), Probable pectinesterase 48 (PME48), Probable pectinesterase 49 (PME49), Probable pectinesterase 50 (PME50), Pectinesterase, Probable pectinesterase/pectinesterase inhibitor 19 (PME19), Probable pectinesterase/pectinesterase inhibitor 42 (PME42), Probable pectinesterase 15 (PME15), Probable pectinesterase/pectinesterase inhibitor 40 (PME40), Putative pectinesterase 14 (PME14), Pectinesterase (At3g10720), Probable pectinesterase 55 (PME55), Probable pectinesterase/pectinesterase inhibitor 23 (PME23), Pectinesterase 4 (PME4), Putative pectinesterase/pectinesterase inhibitor 22 (PME22), Probable pectinesterase/pectinesterase inhibitor 39 (PME39), Pectinesterase (At3g14310), Pectinesterase/pectinesterase inhibitor 18 (PME18), Putative pectinesterase/pectinesterase inhibitor 43 (PME43), Probable pectinesterase/pectinesterase inhibitor 34 (PME34), Pectinesterase 1 (PME1), Putative pectinesterase 63 (PME63), Putative pectinesterase 10 (PME10), Probable pectinesterase/pectinesterase inhibitor 64 (PME64), Pectinesterase (F14I3.7), Pectinesterase 2 (PME2), Probable pectinesterase 29 (PME29), Pectinesterase, Probable pectinesterase/pectinesterase inhibitor 21 (PME21), Putative pectinesterase/pectinesterase inhibitor 45 (PME45), Probable pectinesterase/pectinesterase inhibitor 12 (PME12), Probable pectinesterase/pectinesterase inhibitor 44 (PME44), Probable pectinesterase 8 (PME8), Pectinesterase, Pectinesterase/pectinesterase inhibitor 3 (PME3), Pectinesterase 31 (PME31), Probable pectinesterase/pectinesterase inhibitor 25 (PME25), Probable pectinesterase/pectinesterase inhibitor 51 (PME51), Probable pectinesterase/pectinesterase inhibitor 58 (PME58), Putative pectinesterase 57 (PME57), Pectinesterase (At3g62170), Probable pectinesterase/pectinesterase inhibitor 20 (PME20), Pectinesterase (T27B3.30), Probable pectinesterase/pectinesterase inhibitor 60 (PME60), Probable pectinesterase/pectinesterase inhibitor 59 (PME59), Pectinesterase QRT1 (QRT1), Putative pectinesterase 11 (PME11), Pectinesterase PPME1 (PPME1), Probable pectinesterase/pectinesterase inhibitor 32 (PME32), Probable pectinesterase/pectinesterase inhibitor 33 (PME33), Probable pectinesterase/pectinesterase inhibitor 36 (PME36), Probable pectinesterase/pectinesterase inhibitor 13 (PME13), Putative pectinesterase 52 (PME52), Pectinesterase, Probable pectinesterase/pectinesterase inhibitor 54 (PME54), Pectinesterase, Pectinesterase (At1g53840), Probable pectinesterase/pectinesterase inhibitor 16 (PME16), Pectinesterase 5 (PME5), Probable pectinesterase 30 (PME30), Probable pectinesterase/pectinesterase inhibitor VGDH2 (VGDH2), Putative pectinesterase/pectinesterase inhibitor 24 (PME24), Putative pectinesterase/pectinesterase inhibitor 26 (PME26), Probable pectinesterase/pectinesterase inhibitor 35 (PME35), Probable pectinesterase 68 (PME68), Pectinesterase, Probable pectinesterase 67 (PME67), Putative pectinesterase/pectinesterase inhibitor 38 (PME38), Probable pectinesterase 56 (PME56), Pectinesterase, Probable pectinesterase/pectinesterase inhibitor 47 (PME47), Putative pectinesterase/pectinesterase inhibitor 28 (PME28), Probable pectinesterase 53 (PME53), Probable pectinesterase/pectinesterase inhibitor 46 (PME46), Probable pectinesterase/pectinesterase inhibitor 17 (PME17), Probable pectinesterase/pectinesterase inhibitor 41 (PME41), Probable pectinesterase/pectinesterase inhibitor 61 (PME61), Probable pectinesterase 66 (PME66), Probable pectinesterase/pectinesterase inhibitor 6 (PME6)
  2. Pectate lyase (T26I12.20), Probable pectate lyase 7 (At3g01270), Probable pectate lyase 18 (At4g24780), Probable pectate lyase 16 (At4g22080), Putative pectate lyase 17 (At4g22090), Putative pectate lyase 14 (At4g13210), Pectate lyase (At3g55140), Probable pectate lyase 20 (At5g48900), Probable pectate lyase 6 (At2g02720), Pectate lyase (At1g14420), Pectate lyase (At3g01270), Pectate lyase (At2g02720), Probable pectate lyase 22 (At5g63180), Pectate lyase (T5E8_80), Pectate lyase (At3g01270), Pectate lyase (At3g55140), Putative pectate lyase 2 (At1g11920), Pectate lyase (At3g07010), Pectate lyase, Probable pectate lyase 8 (At3g07010), Probable pectate lyase 4 (At1g30350), Probable pectate lyase 19 (At5g15110), Pectate lyase (F11F8_12), Probable pectate lyase 13 (PMR6), Probable pectate lyase 3 (AT59), Probable pectate lyase 5 (At1g67750), Putative pectate lyase 21 (At5g55720), Pectate lyase (At4g13210), Probable pectate lyase 12 (At3g53190), Pectate lyase (At4g24780), Pectate lyase (At5g04310), Pectate lyase (At4g13710), Probable pectate lyase 15 (At4g13710), Pectate lyase (At3g53190), Pectate lyase (At3g01270), Putative pectate lyase 11 (At3g27400), Pectate lyase (At5g04310), Pectate lyase (At3g07010), Probable pectate lyase 9 (At3g24230), Probable pectate lyase 1 (At1g04680), Probable pectate lyase 10 (At3g24670)
  3. no protein annotated in this organism
  4. no protein annotated in this organism
  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
Binding sitei356 – 3561Substrate; for pectinesterase activityBy similarity
Binding sitei386 – 3861Substrate; for pectinesterase activityBy similarity
Sitei408 – 4081Transition state stabilizerBy similarity
Active sitei409 – 4091Proton donor; for pectinesterase activityPROSITE-ProRule annotation
Active sitei430 – 4301Nucleophile; for pectinesterase activityPROSITE-ProRule annotation
Binding sitei498 – 4981Substrate; for pectinesterase activityBy similarity
Binding sitei500 – 5001Substrate; for pectinesterase activityBy similarity

GO - Molecular functioni

GO - Biological processi

  • cell wall modification Source: InterPro
  • defense response to Gram-negative bacterium Source: TAIR
  • pectin catabolic process Source: UniProtKB-UniPathway
  • response to fungus Source: TAIR
  • response to nematode Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl esterase, Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation

Enzyme and pathway databases

BioCyciARA:AT3G14310-MONOMER.
UniPathwayiUPA00545; UER00823.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectinesterase/pectinesterase inhibitor 3
Including the following 2 domains:
Pectinesterase inhibitor 3
Alternative name(s):
Pectin methylesterase inhibitor 3
Pectinesterase 3 (EC:3.1.1.11)
Short name:
PE 3
Alternative name(s):
Pectin methylesterase 27
Short name:
AtPME27
Pectin methylesterase 3
Gene namesi
Name:PME3
Synonyms:ARATH27
Ordered Locus Names:At3g14310
ORF Names:MLN21.10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G14310.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • cell wall Source: TAIR
  • cytoplasm Source: TAIR
  • plasma membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cell wall, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3535Sequence analysisAdd
BLAST
Chaini36 – 592557Pectinesterase/pectinesterase inhibitor 3PRO_0000371662Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi96 – 961N-linked (GlcNAc...)Sequence analysis
Glycosylationi215 – 2151N-linked (GlcNAc...)Sequence analysis
Disulfide bondi423 ↔ 443By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiO49006.
PRIDEiO49006.

Expressioni

Tissue specificityi

Expressed in leaves, stems, flowers and siliques.2 Publications

Developmental stagei

Expressed throughout silique development.1 Publication

Gene expression databases

GenevisibleiO49006. AT.

Interactioni

Protein-protein interaction databases

BioGridi5985. 2 interactions.
STRINGi3702.AT3G14310.1.

Structurei

3D structure databases

ProteinModelPortaliO49006.
SMRiO49006. Positions 274-592.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni53 – 212160Pectinesterase inhibitor 3Add
BLAST
Regioni281 – 578298Pectinesterase 3Add
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the PMEI family.Curated
In the C-terminal section; belongs to the pectinesterase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IF38. Eukaryota.
COG4677. LUCA.
HOGENOMiHOG000217409.
InParanoidiO49006.
KOiK01051.
OMAiKFLARDI.
PhylomeDBiO49006.

Family and domain databases

Gene3Di1.20.140.40. 1 hit.
2.160.20.10. 1 hit.
InterProiIPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
IPR033131. Pectinesterase_Asp_AS.
IPR000070. Pectinesterase_cat.
IPR006501. Pectinesterase_inhib_dom.
IPR018040. Pectinesterase_Tyr_AS.
[Graphical view]
PfamiPF01095. Pectinesterase. 1 hit.
PF04043. PMEI. 1 hit.
[Graphical view]
SMARTiSM00856. PMEI. 1 hit.
[Graphical view]
SUPFAMiSSF101148. SSF101148. 1 hit.
SSF51126. SSF51126. 1 hit.
TIGRFAMsiTIGR01614. PME_inhib. 1 hit.
PROSITEiPS00800. PECTINESTERASE_1. 1 hit.
PS00503. PECTINESTERASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O49006-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPSMKEIFS KDNFKKNKKL VLLSAAVALL FVAAVAGISA GASKANEKRT
60 70 80 90 100
LSPSSHAVLR SSCSSTRYPE LCISAVVTAG GVELTSQKDV IEASVNLTIT
110 120 130 140 150
AVEHNYFTVK KLIKKRKGLT PREKTALHDC LETIDETLDE LHETVEDLHL
160 170 180 190 200
YPTKKTLREH AGDLKTLISS AITNQETCLD GFSHDDADKQ VRKALLKGQI
210 220 230 240 250
HVEHMCSNAL AMIKNMTDTD IANFEQKAKI TSNNRKLKEE NQETTVAVDI
260 270 280 290 300
AGAGELDSEG WPTWLSAGDR RLLQGSGVKA DATVAADGSG TFKTVAAAVA
310 320 330 340 350
AAPENSNKRY VIHIKAGVYR ENVEVAKKKK NIMFMGDGRT RTIITGSRNV
360 370 380 390 400
VDGSTTFHSA TVAAVGERFL ARDITFQNTA GPSKHQAVAL RVGSDFSAFY
410 420 430 440 450
NCDMLAYQDT LYVHSNRQFF VKCLIAGTVD FIFGNAAVVL QDCDIHARRP
460 470 480 490 500
NSGQKNMVTA QGRTDPNQNT GIVIQKCRIG ATSDLQSVKG SFPTYLGRPW
510 520 530 540 550
KEYSQTVIMQ SAISDVIRPE GWSEWTGTFA LNTLTYREYS NTGAGAGTAN
560 570 580 590
RVKWRGFKVI TAAAEAQKYT AGQFIGGGGW LSSTGFPFSL GL
Length:592
Mass (Da):64,256
Last modified:May 5, 2009 - v2
Checksum:i32AFAF1E6C471B2F
GO

Sequence cautioni

The sequence AAL24278.1 differs from that shown. Reason: Frameshift at position 172. Curated
The sequence BAD94011.1 differs from that shown.Intron retention.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti81 – 822GV → AC in AAC72288 (PubMed:9767082).Curated
Sequence conflicti280 – 2801A → R in AAC72288 (PubMed:9767082).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF033204 Genomic DNA. Translation: AAC72288.1.
AB022220 Genomic DNA. Translation: BAB01037.1.
CP002686 Genomic DNA. Translation: AEE75500.1.
AY037184 mRNA. Translation: AAK59769.1.
AY052252 mRNA. Translation: AAK97722.1.
AY143950 mRNA. Translation: AAN28889.1.
AY058892 mRNA. Translation: AAL24278.1. Frameshift.
AK221816 mRNA. Translation: BAD94011.1. Sequence problems.
RefSeqiNP_188048.1. NM_112289.2.
UniGeneiAt.43283.
At.6066.
At.67322.
At.74977.

Genome annotation databases

EnsemblPlantsiAT3G14310.1; AT3G14310.1; AT3G14310.
GeneIDi820651.
GrameneiAT3G14310.1; AT3G14310.1; AT3G14310.
KEGGiath:AT3G14310.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF033204 Genomic DNA. Translation: AAC72288.1.
AB022220 Genomic DNA. Translation: BAB01037.1.
CP002686 Genomic DNA. Translation: AEE75500.1.
AY037184 mRNA. Translation: AAK59769.1.
AY052252 mRNA. Translation: AAK97722.1.
AY143950 mRNA. Translation: AAN28889.1.
AY058892 mRNA. Translation: AAL24278.1. Frameshift.
AK221816 mRNA. Translation: BAD94011.1. Sequence problems.
RefSeqiNP_188048.1. NM_112289.2.
UniGeneiAt.43283.
At.6066.
At.67322.
At.74977.

3D structure databases

ProteinModelPortaliO49006.
SMRiO49006. Positions 274-592.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi5985. 2 interactions.
STRINGi3702.AT3G14310.1.

Proteomic databases

PaxDbiO49006.
PRIDEiO49006.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G14310.1; AT3G14310.1; AT3G14310.
GeneIDi820651.
GrameneiAT3G14310.1; AT3G14310.1; AT3G14310.
KEGGiath:AT3G14310.

Organism-specific databases

TAIRiAT3G14310.

Phylogenomic databases

eggNOGiENOG410IF38. Eukaryota.
COG4677. LUCA.
HOGENOMiHOG000217409.
InParanoidiO49006.
KOiK01051.
OMAiKFLARDI.
PhylomeDBiO49006.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00823.
BioCyciARA:AT3G14310-MONOMER.

Miscellaneous databases

PROiO49006.

Gene expression databases

GenevisibleiO49006. AT.

Family and domain databases

Gene3Di1.20.140.40. 1 hit.
2.160.20.10. 1 hit.
InterProiIPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
IPR033131. Pectinesterase_Asp_AS.
IPR000070. Pectinesterase_cat.
IPR006501. Pectinesterase_inhib_dom.
IPR018040. Pectinesterase_Tyr_AS.
[Graphical view]
PfamiPF01095. Pectinesterase. 1 hit.
PF04043. PMEI. 1 hit.
[Graphical view]
SMARTiSM00856. PMEI. 1 hit.
[Graphical view]
SUPFAMiSSF101148. SSF101148. 1 hit.
SSF51126. SSF51126. 1 hit.
TIGRFAMsiTIGR01614. PME_inhib. 1 hit.
PROSITEiPS00800. PECTINESTERASE_1. 1 hit.
PS00503. PECTINESTERASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the pectin methylesterase-like gene AtPME3: a new member of a gene family comprising at least 12 genes in Arabidopsis thaliana."
    Micheli F., Holliger C., Goldberg R., Richard L.
    Gene 220:13-20(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY.
  2. "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones."
    Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.
    DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Pectin methylesterases: sequence-structural features and phylogenetic relationships."
    Markovic O., Janecek S.
    Carbohydr. Res. 339:2281-2295(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  7. "Comprehensive expression profiling of the pectin methylesterase gene family during silique development in Arabidopsis thaliana."
    Louvet R., Cavel E., Gutierrez L., Guenin S., Roger D., Gillet F., Guerineau F., Pelloux J.
    Planta 224:782-791(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiPME3_ARATH
AccessioniPrimary (citable) accession number: O49006
Secondary accession number(s): Q56X61, Q93YZ2, Q9LUL7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 5, 2009
Last sequence update: May 5, 2009
Last modified: July 6, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The PMEI region may act as an autoinhibitory domain and prevent untimely PME activity during transport.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.