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Protein

Probable pectinesterase/pectinesterase inhibitor VGDH2

Gene

VGDH2

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), Probable pectinesterase/pectinesterase inhibitor 64 (PME64), Putative pectinesterase 10 (PME10), 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 (AXX17_AT1G48300), Pectinesterase (At1g53840), Pectinesterase 5 (PME5), Probable pectinesterase/pectinesterase inhibitor 16 (PME16), Probable pectinesterase 30 (PME30), Probable pectinesterase/pectinesterase inhibitor VGDH2 (VGDH2), Putative pectinesterase/pectinesterase inhibitor 24 (PME24), Putative pectinesterase/pectinesterase inhibitor 26 (PME26), Probable pectinesterase 68 (PME68), Probable pectinesterase/pectinesterase inhibitor 35 (PME35), Pectinesterase, Probable pectinesterase 67 (PME67), Putative pectinesterase/pectinesterase inhibitor 38 (PME38), Probable pectinesterase 56 (PME56), Pectinesterase, 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), 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 sitei353 – 3531Substrate; for pectinesterase activityBy similarity
Binding sitei383 – 3831Substrate; for pectinesterase activityBy similarity
Sitei405 – 4051Transition state stabilizerBy similarity
Active sitei406 – 4061Proton donor; for pectinesterase activityPROSITE-ProRule annotation
Active sitei427 – 4271Nucleophile; for pectinesterase activityPROSITE-ProRule annotation
Binding sitei496 – 4961Substrate; for pectinesterase activityBy similarity
Binding sitei498 – 4981Substrate; for pectinesterase activityBy similarity

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

BioCyciARA:AT3G62170-MONOMER.
BRENDAi3.1.1.11. 399.
UniPathwayiUPA00545; UER00823.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pectinesterase/pectinesterase inhibitor VGDH2
Alternative name(s):
VANGUARD1-like protein 2
Short name:
VGD1-like protein 2
Including the following 2 domains:
Pectinesterase inhibitor VGDH2
Alternative name(s):
Pectin methylesterase inhibitor VGDH2
Pectinesterase VGDH2 (EC:3.1.1.11)
Short name:
PE VGDH2
Alternative name(s):
Pectin methylesterase 37
Short name:
AtPME37
Pectin methylesterase VGDH2
Gene namesi
Name:VGDH2
Synonyms:ARATH37
Ordered Locus Names:At3g62170
ORF Names:T17J13.130
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G62170.

Subcellular locationi

GO - Cellular componenti

  • cell periphery Source: GO_Central
  • cell wall Source: UniProtKB-SubCell
  • extracellular region Source: UniProtKB-KW
  • pollen tube Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cell wall, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2222Sequence analysisAdd
BLAST
Chaini23 – 588566Probable pectinesterase/pectinesterase inhibitor VGDH2PRO_0000023478Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi93 – 931N-linked (GlcNAc...)Sequence analysis
Glycosylationi107 – 1071N-linked (GlcNAc...)Sequence analysis
Glycosylationi213 – 2131N-linked (GlcNAc...)Sequence analysis
Glycosylationi231 – 2311N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ5MFV6.
PRIDEiQ5MFV6.

Expressioni

Tissue specificityi

Expressed in flower buds, pollen grains and pollen tubes.1 Publication

Gene expression databases

GenevisibleiQ5MFV6. AT.

Interactioni

Protein-protein interaction databases

BioGridi10704. 1 interaction.
MINTiMINT-8069886.
STRINGi3702.AT3G62170.1.

Structurei

3D structure databases

ProteinModelPortaliQ5MFV6.
SMRiQ5MFV6. Positions 278-588.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni42 – 193152Pectinesterase inhibitor VGDH2Add
BLAST
Regioni276 – 574299Pectinesterase VGDH2Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi262 – 27110Poly-Gly

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

eggNOGiENOG410JB1S. Eukaryota.
COG4677. LUCA.
HOGENOMiHOG000217409.
InParanoidiQ5MFV6.
OMAiGPANWIQ.
OrthoDBiEOG093606UI.
PhylomeDBiQ5MFV6.

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.

Q5MFV6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVGKVVVSV ASLLLVVGVA IGVITFVNKG GGANGDSNGP INSHQKAVQT
60 70 80 90 100
ICQSTTDQGS CAKTLDPVKS DDPSKLVKAF LMATKDAITK SSNFTASTEG
110 120 130 140 150
GMGTNMNATS KAVLDYCKRV LMYALEDLET IVEEMGEDLQ QSGTKLDQLK
160 170 180 190 200
QWLTGVFNYQ TDCLDDIEEV ELKKIMGEGI SNSKVLTSNA IDIFHSVVTA
210 220 230 240 250
MAQMGVKVDD MKNITMGAGA GGAARRLLED NDSKGLPKWF SGKDRKLMAK
260 270 280 290 300
AGRGAPAGGD DGIGEGGGGG GKIKATHVVA KDGSGQFKTI SEAVMACPDK
310 320 330 340 350
NPGRCIIHIK AGIYNEQVRI PKKKNNIFMF GDGATQTIIT FDRSVKLSPG
360 370 380 390 400
TTTSLSGTVQ VESEGFMAKW IGFKNTAGPL GHQAVALRVN GDRAVIFNCR
410 420 430 440 450
FDGYQDTLYV NNGRQFYRNI VVSGTVDFIF GKSATVIQNS LILVRKGSPG
460 470 480 490 500
QSNYVTADGN EKGAAMKIGI VLHNCRIIPD KELEADKLTI KSYLGRPWKK
510 520 530 540 550
FATTVIIGTE IGDLIKPEGW TEWQGEQNHK TAKYIEFNNR GPGAATTQRP
560 570 580
PWVKVAKSAA EVETYTVANW VGPANWIQEA NVPVQLGL
Length:588
Mass (Da):62,958
Last modified:March 15, 2005 - v2
Checksum:iBAEF057677EA7848
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti53 – 531Q → L in AAV91510 (PubMed:15659637).Curated
Sequence conflicti165 – 1651D → G in AAV91510 (PubMed:15659637).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY830950 mRNA. Translation: AAV91510.1.
AL138651 Genomic DNA. Translation: CAB71877.1.
CP002686 Genomic DNA. Translation: AEE80318.1.
AY093237 mRNA. Translation: AAM13236.1.
AY084580 mRNA. Translation: AAM61145.1.
PIRiT48009.
RefSeqiNP_191776.1. NM_116082.2.
UniGeneiAt.34168.

Genome annotation databases

EnsemblPlantsiAT3G62170.1; AT3G62170.1; AT3G62170.
GeneIDi825390.
GrameneiAT3G62170.1; AT3G62170.1; AT3G62170.
KEGGiath:AT3G62170.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY830950 mRNA. Translation: AAV91510.1.
AL138651 Genomic DNA. Translation: CAB71877.1.
CP002686 Genomic DNA. Translation: AEE80318.1.
AY093237 mRNA. Translation: AAM13236.1.
AY084580 mRNA. Translation: AAM61145.1.
PIRiT48009.
RefSeqiNP_191776.1. NM_116082.2.
UniGeneiAt.34168.

3D structure databases

ProteinModelPortaliQ5MFV6.
SMRiQ5MFV6. Positions 278-588.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi10704. 1 interaction.
MINTiMINT-8069886.
STRINGi3702.AT3G62170.1.

Proteomic databases

PaxDbiQ5MFV6.
PRIDEiQ5MFV6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G62170.1; AT3G62170.1; AT3G62170.
GeneIDi825390.
GrameneiAT3G62170.1; AT3G62170.1; AT3G62170.
KEGGiath:AT3G62170.

Organism-specific databases

TAIRiAT3G62170.

Phylogenomic databases

eggNOGiENOG410JB1S. Eukaryota.
COG4677. LUCA.
HOGENOMiHOG000217409.
InParanoidiQ5MFV6.
OMAiGPANWIQ.
OrthoDBiEOG093606UI.
PhylomeDBiQ5MFV6.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00823.
BioCyciARA:AT3G62170-MONOMER.
BRENDAi3.1.1.11. 399.

Miscellaneous databases

PROiQ5MFV6.

Gene expression databases

GenevisibleiQ5MFV6. 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...

Entry informationi

Entry nameiPME37_ARATH
AccessioniPrimary (citable) accession number: Q5MFV6
Secondary accession number(s): Q9M1Q7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: September 7, 2016
This is version 94 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.