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Protein

Pectinesterase 5

Gene

PME5

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

Functioni

Acts in the modification of cell walls via demethylesterification of cell wall pectin. Plays an important role in growth of pollen tubes in female floral tissues, possibly via enhancing the interaction between the pollen tube and female floral tissues by modification of the cell walls.1 Publication

Catalytic activityi

Pectin + n H2O = n methanol + pectate.

Pathway: 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), Probable pectinesterase/pectinesterase inhibitor 19 (PME19), Probable pectinesterase/pectinesterase inhibitor 42 (PME42), Probable pectinesterase 15 (PME15), Putative pectinesterase 14 (PME14), Probable pectinesterase/pectinesterase inhibitor 40 (PME40), 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/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 2 (PME2), Probable pectinesterase 29 (PME29), 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 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), Probable pectinesterase/pectinesterase inhibitor 20 (PME20), Probable pectinesterase/pectinesterase inhibitor 60 (PME60), Pectinesterase QRT1 (QRT1), Probable pectinesterase/pectinesterase inhibitor 59 (PME59), 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), 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), Probable pectinesterase 67 (PME67), Putative pectinesterase/pectinesterase inhibitor 38 (PME38), Probable pectinesterase 56 (PME56), Putative pectinesterase/pectinesterase inhibitor 28 (PME28), Probable pectinesterase/pectinesterase inhibitor 47 (PME47), Probable pectinesterase/pectinesterase inhibitor 46 (PME46), Probable pectinesterase 53 (PME53), 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), Pectate lyase, 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 sitei360 – 3601SubstrateBy similarity
Binding sitei390 – 3901SubstrateBy similarity
Sitei412 – 4121Transition state stabilizerBy similarity
Active sitei413 – 4131Proton donorPROSITE-ProRule annotation
Active sitei434 – 4341NucleophilePROSITE-ProRule annotation
Binding sitei503 – 5031SubstrateBy similarity
Binding sitei505 – 5051SubstrateBy similarity

GO - Molecular functioni

  • aspartyl esterase activity Source: UniProtKB-KW
  • enzyme inhibitor activity Source: InterPro
  • pectinesterase activity Source: UniProtKB

GO - Biological processi

  • cell wall modification Source: InterPro
  • pectin catabolic process Source: UniProtKB-UniPathway
  • pollen tube growth Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl esterase, Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation

Enzyme and pathway databases

BioCyciARA:AT2G47040-MONOMER.
BRENDAi3.1.1.11. 399.
UniPathwayiUPA00545; UER00823.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectinesterase 5 (EC:3.1.1.11)
Short name:
PE 5
Alternative name(s):
Pectin methylesterase 5
Short name:
AtPME5
Pectin methylesterase 67
Short name:
AtPME67
Protein VANGUARD 1
Gene namesi
Name:PME5
Synonyms:ARATH67, VGD1
Ordered Locus Names:At2g47040
ORF Names:F14M4.13
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G47040.

Subcellular locationi

GO - Cellular componenti

  • cell wall Source: UniProtKB-SubCell
  • extracellular region Source: UniProtKB-KW
  • Golgi membrane Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
  • pollen tube Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell wall, Golgi apparatus, Membrane, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence AnalysisAdd
BLAST
Chaini25 – 595571Pectinesterase 5PRO_0000023477Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi86 – 861N-linked (GlcNAc...)Sequence Analysis
Glycosylationi206 – 2061N-linked (GlcNAc...)Sequence Analysis
Glycosylationi349 – 3491N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ5MFV8.
PRIDEiQ5MFV8.

Expressioni

Tissue specificityi

Expressed in pollen grains and pollen tubes.1 Publication

Developmental stagei

Expressed throughout silique development.1 Publication

Interactioni

Subunit structurei

Interacts with SBT6.1.1 Publication

Protein-protein interaction databases

BioGridi4653. 2 interactions.
STRINGi3702.AT2G47040.1.

Structurei

3D structure databases

ProteinModelPortaliQ5MFV8.
SMRiQ5MFV8. Positions 285-595.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi243 – 2464RRLL cleavage motif1 Publication
Motifi263 – 2664RKLM cleavage motif1 Publication

Domaini

The PMEI region may act as an autoinhibitory domain and prevent untimely PME activity during transport. The PMEI region is cleaved by SBT6.1 (S1P) in the Golgi apparatus prior to cell wall targeting.1 Publication

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

eggNOGiCOG4677.
HOGENOMiHOG000217409.
InParanoidiQ5MFV8.
PhylomeDBiQ5MFV8.

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.
IPR018040. Pectinesterase_AS.
IPR000070. Pectinesterase_cat.
IPR006501. Pectinesterase_inhib_dom.
[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.

Q5MFV8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIGKVVVSVA SILLIVGVAI GVVAYINKNG DANLSPQMKA VRGICEATSD
60 70 80 90 100
KASCVKTLEP VKSDDPNKLI KAFMLATRDA ITQSSNFTGK TEGNLGSGIS
110 120 130 140 150
PNNKAVLDYC KKVFMYALED LSTIVEEMGE DLNQIGSKID QLKQWLTGVY
160 170 180 190 200
NYQTDCLDDI EEDDLRKTIG EGIASSKILT SNAIDIFHTV VSAMAKLNLK
210 220 230 240 250
VEDFKNMTGG IFAPSDKGAA PVNKGTPPVA DDSPVADPDG PARRLLEDID
260 270 280 290 300
ETGIPTWVSG ADRKLMTKAG RGSNDGGARI RATFVVAKDG SGQFKTVQQA
310 320 330 340 350
VNACPEKNPG RCIIHIKAGI YREQVIIPKK KNNIFMFGDG ARKTVISYNR
360 370 380 390 400
SVKLSPGTTT SLSGTVQVES EGFMAKWIGF KNTAGPMGHQ AVAIRVNGDR
410 420 430 440 450
AVIFNCRFDG YQDTLYVNNG RQFYRNIVVS GTVDFIFGKS ATVIQNSLIV
460 470 480 490 500
VRKGNKGQFN TVTADGNEKG LAMKIGIVLQ NCRIVPDKKL AAERLIVESY
510 520 530 540 550
LGRPWKKFST TVIINSEIGD VIRPEGWKIW DGESFHKSCR YVEYNNRGPG
560 570 580 590
AITNRRVNWV KIARSAAEVN DFTVANWLGP INWIQEANVP VTLGL
Length:595
Mass (Da):64,728
Last modified:March 15, 2005 - v2
Checksum:iE314E53201F3CD77
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti50 – 501D → V in AAV91508 (PubMed:15659637).Curated
Sequence conflicti93 – 931G → E in CAB58974 (Ref. 2) Curated
Sequence conflicti138 – 1381K → E in AAV91508 (PubMed:15659637).Curated
Sequence conflicti267 – 2671T → A in AAV91508 (PubMed:15659637).Curated
Sequence conflicti267 – 2671T → A in CAB58974 (Ref. 2) Curated
Sequence conflicti537 – 5371K → Q in AAV91508 (PubMed:15659637).Curated
Sequence conflicti545 – 5451N → S in AAV91508 (PubMed:15659637).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY830948 mRNA. Translation: AAV91508.1.
AJ250430 mRNA. Translation: CAB58974.1.
AC004411 Genomic DNA. Translation: AAC34240.1.
CP002685 Genomic DNA. Translation: AEC10791.1.
AY091768 mRNA. Translation: AAM10316.1.
BT001120 mRNA. Translation: AAN64511.1.
PIRiT02183.
T52327.
RefSeqiNP_182227.1. NM_130272.3.
UniGeneiAt.24875.

Genome annotation databases

EnsemblPlantsiAT2G47040.1; AT2G47040.1; AT2G47040.
GeneIDi819318.
KEGGiath:AT2G47040.

Cross-referencesi

Web resourcesi

Protein Spotlight

When tough is soft - Issue 106 of June 2009

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY830948 mRNA. Translation: AAV91508.1.
AJ250430 mRNA. Translation: CAB58974.1.
AC004411 Genomic DNA. Translation: AAC34240.1.
CP002685 Genomic DNA. Translation: AEC10791.1.
AY091768 mRNA. Translation: AAM10316.1.
BT001120 mRNA. Translation: AAN64511.1.
PIRiT02183.
T52327.
RefSeqiNP_182227.1. NM_130272.3.
UniGeneiAt.24875.

3D structure databases

ProteinModelPortaliQ5MFV8.
SMRiQ5MFV8. Positions 285-595.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4653. 2 interactions.
STRINGi3702.AT2G47040.1.

Proteomic databases

PaxDbiQ5MFV8.
PRIDEiQ5MFV8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G47040.1; AT2G47040.1; AT2G47040.
GeneIDi819318.
KEGGiath:AT2G47040.

Organism-specific databases

GeneFarmi443. 8.
TAIRiAT2G47040.

Phylogenomic databases

eggNOGiCOG4677.
HOGENOMiHOG000217409.
InParanoidiQ5MFV8.
PhylomeDBiQ5MFV8.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00823.
BioCyciARA:AT2G47040-MONOMER.
BRENDAi3.1.1.11. 399.

Miscellaneous databases

PROiQ5MFV8.

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.
IPR018040. Pectinesterase_AS.
IPR000070. Pectinesterase_cat.
IPR006501. Pectinesterase_inhib_dom.
[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. "VANGUARD1 encodes a pectin methylesterase that enhances pollen tube growth in the Arabidopsis style and transmitting tract."
    Jiang L., Yang S.-L., Xie L.-F., Puah C.S., Zhang X.-Q., Yang W.-C., Sundaresan V., Ye D.
    Plant Cell 17:584-596(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: cv. Landsberg erecta.
  2. "Characterization of a flower-specific gene encoding pectin methylesterase in Arabidopsis thaliana."
    Torki M., Mache R., Mandaron P., Falconet D.
    Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Flower bud.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "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.
  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: DEVELOPMENTAL STAGE.
  8. "The N-terminal pro region mediates retention of unprocessed type-I PME in the Golgi apparatus."
    Wolf S., Rausch T., Greiner S.
    Plant J. 58:361-375(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SBT6.1, SUBCELLULAR LOCATION, DOMAIN, CLEAVAGE BY SBT6.1.

Entry informationi

Entry nameiPME5_ARATH
AccessioniPrimary (citable) accession number: Q5MFV8
Secondary accession number(s): O80721, Q9SMV9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: June 24, 2015
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.