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Protein

Probable pectate lyase 1

Gene

At1g04680

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

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), 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
Metal bindingi227 – 2271CalciumBy similarity
Metal bindingi251 – 2511CalciumBy similarity
Metal bindingi255 – 2551CalciumBy similarity
Active sitei307 – 3071Sequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT1G04680-MONOMER.
UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pectate lyase 1 (EC:4.2.2.2)
Alternative name(s):
Pectate lyase A1
Gene namesi
Ordered Locus Names:At1g04680
ORF Names:T1G11.7, T1G11_6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G04680.

Subcellular locationi

GO - Cellular componenti

  • membrane Source: TAIR
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2020Sequence analysisAdd
BLAST
Chaini21 – 431411Probable pectate lyase 1PRO_0000024865Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi23 – 231N-linked (GlcNAc...)Sequence analysis
Glycosylationi28 – 281N-linked (GlcNAc...)Sequence analysis
Glycosylationi65 – 651N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ940Q1.
PRIDEiQ940Q1.

Expressioni

Tissue specificityi

Expressed in flowers, but not in leaves.1 Publication

Gene expression databases

GenevisibleiQ940Q1. AT.

Interactioni

Protein-protein interaction databases

BioGridi24687. 1 interaction.
STRINGi3702.AT1G04680.1.

Structurei

3D structure databases

ProteinModelPortaliQ940Q1.
SMRiQ940Q1. Positions 81-421.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 1 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410JTUD. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ940Q1.
KOiK01728.
OMAiEWNQHAV.
OrthoDBiEOG09360B0M.
PhylomeDBiQ940Q1.

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.

Q940Q1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVLPTWLLA MMCLLFFVGA MENTTHDNIS SLPRSDETEW NQHAVTNPDE
60 70 80 90 100
VADEVLALTE MSVRNHTERR KLGYFTCGTG NPIDDCWRCD PNWHKNRKRL
110 120 130 140 150
ADCGIGFGRN AIGGRDGRFY VVTDPRDDNP VNPRPGTLRH AVIQDRPLWI
160 170 180 190 200
VFKRDMVIQL KQELIVNSFK TIDGRGANVH IANGGCITIQ FVTNVIVHGL
210 220 230 240 250
HIHDCKPTGN AMVRSSETHF GWRTMADGDA ISIFGSSHVW IDHNSLSHCA
260 270 280 290 300
DGLVDAVMGS TAITISNNHL THHNEVMLLG HSDSYMRDKA MQVTIAYNHF
310 320 330 340 350
GVGLIQRMPR CRHGYFHVVN NDYTHWEMYA IGGSANPTIN SQGNRYAAPK
360 370 380 390 400
NPFAKEVTKR VDTPASHWKG WNWRSEGDLL QNGAYFTSSG AAASGSYARA
410 420 430
SSLSAKSSSL VGHITSDAGA LPCRRGRQCS S
Length:431
Mass (Da):47,771
Last modified:June 16, 2003 - v2
Checksum:i241D3FD68D55C832
GO

Sequence cautioni

The sequence AAL06861 differs from that shown. Reason: Frameshift at position 351. Curated
The sequence AAL47400 differs from that shown. Reason: Frameshift at position 351. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti151 – 1511V → I in AAB69760 (PubMed:9278171).Curated
Sequence conflicti208 – 2081Missing in AAB69760 (PubMed:9278171).Curated
Sequence conflicti255 – 2573DAV → ERS in AAB69760 (PubMed:9278171).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC002376 Genomic DNA. Translation: AAB80622.1.
CP002684 Genomic DNA. Translation: AEE27732.1.
AY065034 mRNA. Translation: AAL57671.1.
AY054200 mRNA. Translation: AAL06861.1. Frameshift.
AY066033 mRNA. Translation: AAL47400.1. Frameshift.
AY087724 mRNA. Translation: AAM65261.1.
U83620 Genomic DNA. Translation: AAB69760.1.
PIRiF86179.
RefSeqiNP_563715.1. NM_100348.3.
UniGeneiAt.10458.

Genome annotation databases

EnsemblPlantsiAT1G04680.1; AT1G04680.1; AT1G04680.
GeneIDi839452.
GrameneiAT1G04680.1; AT1G04680.1; AT1G04680.
KEGGiath:AT1G04680.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC002376 Genomic DNA. Translation: AAB80622.1.
CP002684 Genomic DNA. Translation: AEE27732.1.
AY065034 mRNA. Translation: AAL57671.1.
AY054200 mRNA. Translation: AAL06861.1. Frameshift.
AY066033 mRNA. Translation: AAL47400.1. Frameshift.
AY087724 mRNA. Translation: AAM65261.1.
U83620 Genomic DNA. Translation: AAB69760.1.
PIRiF86179.
RefSeqiNP_563715.1. NM_100348.3.
UniGeneiAt.10458.

3D structure databases

ProteinModelPortaliQ940Q1.
SMRiQ940Q1. Positions 81-421.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi24687. 1 interaction.
STRINGi3702.AT1G04680.1.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Proteomic databases

PaxDbiQ940Q1.
PRIDEiQ940Q1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G04680.1; AT1G04680.1; AT1G04680.
GeneIDi839452.
GrameneiAT1G04680.1; AT1G04680.1; AT1G04680.
KEGGiath:AT1G04680.

Organism-specific databases

TAIRiAT1G04680.

Phylogenomic databases

eggNOGiENOG410JTUD. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ940Q1.
KOiK01728.
OMAiEWNQHAV.
OrthoDBiEOG09360B0M.
PhylomeDBiQ940Q1.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BioCyciARA:AT1G04680-MONOMER.

Miscellaneous databases

PROiQ940Q1.

Gene expression databases

GenevisibleiQ940Q1. 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...

Entry informationi

Entry nameiPLY1_ARATH
AccessioniPrimary (citable) accession number: Q940Q1
Secondary accession number(s): O23017, O23666
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: June 16, 2003
Last modified: September 7, 2016
This is version 110 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. 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.