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Protein

Probable pectate lyase 13

Gene

PMR6

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

Functioni

Susceptibility factor required for infection by most powdery mildews, but not by unrelated pathogens. Exact function not known, but clearly affects cell wall composition.1 Publication

Catalytic activityi

Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.

Cofactori

Ca2+By similarityNote: Binds 1 Ca2+ ion. Required for its activity.By similarity

Pathwayi: pectin degradation

This protein is involved in step 2 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
Metal bindingi217 – 2171CalciumBy similarity
Metal bindingi241 – 2411CalciumBy similarity
Metal bindingi245 – 2451CalciumBy similarity
Active sitei297 – 2971Sequence analysis

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • pectate lyase activity Source: TAIR

GO - Biological processi

  • cell wall modification involved in multidimensional cell growth Source: TAIR
  • defense response, incompatible interaction Source: TAIR
  • pectin catabolic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT3G54920-MONOMER.
UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pectate lyase 13 (EC:4.2.2.2)
Alternative name(s):
Powdery mildew susceptibility protein
Powdery mildew-resistant mutant 6
Gene namesi
Name:PMR6
Ordered Locus Names:At3g54920
ORF Names:F28P10_100
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G54920.

Subcellular locationi

GO - Cellular componenti

  • anchored component of membrane Source: TAIR
  • anchored component of plasma membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi140 – 1401G → D in pmr6-1; strong powdery mildew resistance, cell walls of plants are enriched for pectins with a lower degree of esterification and an alteration in the H bonding environment of cellulose microfibrils. 1 Publication
Mutagenesisi339 – 3391P → L in pmr6-5; strong powdery mildew resistance, cell walls of plants are enriched for pectins with a lower degree of esterification and an alteration in the H bonding environment of cellulose microfibrils. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2222Add
BLAST
Chaini23 – 474452Probable pectate lyase 13PRO_0000024877Add
BLAST
Propeptidei475 – 50127Removed in mature formSequence analysisPRO_0000024878Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi27 – 271N-linked (GlcNAc...)Sequence analysis
Glycosylationi49 – 491N-linked (GlcNAc...)Sequence analysis
Lipidationi474 – 4741GPI-anchor amidated serineSequence analysis

Keywords - PTMi

Glycoprotein, GPI-anchor, Lipoprotein

Proteomic databases

PaxDbiQ93Z04.

PTM databases

iPTMnetiQ93Z04.

Expressioni

Tissue specificityi

Expressed equally in mature leaves, buds, flowers, rosettes and roots.1 Publication

Gene expression databases

GenevisibleiQ93Z04. AT.

Interactioni

Protein-protein interaction databases

BioGridi9973. 3 interactions.
STRINGi3702.AT3G54920.1.

Structurei

3D structure databases

ProteinModelPortaliQ93Z04.
SMRiQ93Z04. Positions 79-411.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi58 – 7417Poly-SerAdd
BLAST
Compositional biasi430 – 4378Poly-Gly
Compositional biasi457 – 4615Poly-Ser

Domaini

The C-terminal domain not found in other pectate lyase-like protein is required for PMR6 function since the pmr6-2 mutation confers resistance by introducing a frameshift in the mature mRNA which eliminates the C-terminal domain.

Sequence similaritiesi

Belongs to the polysaccharide lyase 1 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IGFP. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ93Z04.
KOiK01728.
OMAiSAVHITG.
PhylomeDBiQ93Z04.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR002022. Amb_allergen_dom.
IPR018082. AmbAllergen.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00544. Pec_lyase_C. 1 hit.
[Graphical view]
PRINTSiPR00807. AMBALLERGEN.
SMARTiSM00656. Amb_all. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q93Z04-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLQNFSNTI FLLCLFFTLL SATKPLNLTL PHQHPSPDSV ALHVIRSVNE
60 70 80 90 100
SLARRQLSSP SSSSSSSSSS SSSSCRTGNP IDDCWRCSDA DWSTNRQRLA
110 120 130 140 150
DCSIGFGHGT LGGKNGKIYV VTDSSDNNPT NPTPGTLRYG VIQEEPLWIV
160 170 180 190 200
FSSNMLIRLK QELIINSYKT LDGRGSAVHI TGNGCLTLQY VQHIIIHNLH
210 220 230 240 250
IYDCKPSAGF EKRGRSDGDG ISIFGSQKIW VDHCSMSHCT DGLIDAVMGS
260 270 280 290 300
TAITISNNYF THHDEVMLLG HDDNYAPDTG MQVTIAFNHF GQGLVQRMPR
310 320 330 340 350
CRRGYIHVVN NDFTEWKMYA IGGSGNPTIN SQGNRYSAPS DPSAKEVTKR
360 370 380 390 400
VDSKDDGEWS NWNWRTEGDL MENGAFFVAS GEGMSSMYSK ASSVDPKAAS
410 420 430 440 450
LVDQLTRNAG VFGGPRDDQG QSGNSYSPYG GDGGGGGSSG GSSGGGMDVM
460 470 480 490 500
GGTTRGSSSS SGDDSNVFQM IFGSDAPSRP RLTLLFSLLM ISVLSLSTLL

L
Length:501
Mass (Da):53,929
Last modified:December 1, 2001 - v1
Checksum:i9E0DE36DEF4C7ABB
GO

Sequence cautioni

The sequence CAB41092.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF534079 mRNA. Translation: AAM97687.1.
AL049655 Genomic DNA. Translation: CAB41092.1. Sequence problems.
CP002686 Genomic DNA. Translation: AEE79313.1.
AY058870 mRNA. Translation: AAL24257.1.
AY074331 mRNA. Translation: AAL67027.1.
AY096739 mRNA. Translation: AAM20373.1.
PIRiT06728.
RefSeqiNP_191052.2. NM_115349.5.
UniGeneiAt.3109.

Genome annotation databases

EnsemblPlantsiAT3G54920.1; AT3G54920.1; AT3G54920.
GeneIDi824657.
GrameneiAT3G54920.1; AT3G54920.1; AT3G54920.
KEGGiath:AT3G54920.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF534079 mRNA. Translation: AAM97687.1.
AL049655 Genomic DNA. Translation: CAB41092.1. Sequence problems.
CP002686 Genomic DNA. Translation: AEE79313.1.
AY058870 mRNA. Translation: AAL24257.1.
AY074331 mRNA. Translation: AAL67027.1.
AY096739 mRNA. Translation: AAM20373.1.
PIRiT06728.
RefSeqiNP_191052.2. NM_115349.5.
UniGeneiAt.3109.

3D structure databases

ProteinModelPortaliQ93Z04.
SMRiQ93Z04. Positions 79-411.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi9973. 3 interactions.
STRINGi3702.AT3G54920.1.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

PTM databases

iPTMnetiQ93Z04.

Proteomic databases

PaxDbiQ93Z04.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G54920.1; AT3G54920.1; AT3G54920.
GeneIDi824657.
GrameneiAT3G54920.1; AT3G54920.1; AT3G54920.
KEGGiath:AT3G54920.

Organism-specific databases

TAIRiAT3G54920.

Phylogenomic databases

eggNOGiENOG410IGFP. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ93Z04.
KOiK01728.
OMAiSAVHITG.
PhylomeDBiQ93Z04.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BioCyciARA:AT3G54920-MONOMER.

Miscellaneous databases

PROiQ93Z04.

Gene expression databases

GenevisibleiQ93Z04. AT.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR002022. Amb_allergen_dom.
IPR018082. AmbAllergen.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00544. Pec_lyase_C. 1 hit.
[Graphical view]
PRINTSiPR00807. AMBALLERGEN.
SMARTiSM00656. Amb_all. 1 hit.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "PMR6, a pectate lyase-like gene required for powdery mildew susceptibility in Arabidopsis."
    Vogel J.P., Raab T.K., Schiff C., Somerville S.C.
    Plant Cell 14:2095-2106(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, MUTAGENESIS OF GLY-140 AND PRO-339.
  2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(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.

Entry informationi

Entry nameiPLY13_ARATH
AccessioniPrimary (citable) accession number: Q93Z04
Secondary accession number(s): Q9SV40
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: December 1, 2001
Last modified: June 8, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Pmr6 mutations are pleiotropic, indicating that PMR6 plays a unique role in normal plant growth and development. The increased resistance in mutants is not mediated by the constitutive activation of the SA-dependent or the JA/ethylene-dependent defense pathway.

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.