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Protein

Probable pectate lyase 9

Gene

At3g24230

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), 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 bindingi250 – 2501CalciumBy similarity
Metal bindingi274 – 2741CalciumBy similarity
Metal bindingi278 – 2781CalciumBy similarity
Active sitei330 – 3301Sequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT3G24230-MONOMER.
UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pectate lyase 9 (EC:4.2.2.2)
Gene namesi
Ordered Locus Names:At3g24230
ORF Names:MUJ8.14
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G24230.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2525Sequence analysisAdd
BLAST
Chaini26 – 452427Probable pectate lyase 9PRO_0000024873Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi88 – 881N-linked (GlcNAc...)Sequence analysis
Glycosylationi139 – 1391N-linked (GlcNAc...)Sequence analysis
Glycosylationi214 – 2141N-linked (GlcNAc...)Sequence analysis
Glycosylationi233 – 2331N-linked (GlcNAc...)Sequence analysis
Glycosylationi271 – 2711N-linked (GlcNAc...)Sequence analysis
Glycosylationi281 – 2811N-linked (GlcNAc...)Sequence analysis
Glycosylationi305 – 3051N-linked (GlcNAc...)Sequence analysis
Glycosylationi374 – 3741N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9LRM5.
PRIDEiQ9LRM5.

Expressioni

Gene expression databases

GenevisibleiQ9LRM5. AT.

Interactioni

Protein-protein interaction databases

STRINGi3702.AT3G24230.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LRM5.
SMRiQ9LRM5. Positions 104-414.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 1 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410JSZY. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ9LRM5.
KOiK01728.
OMAiDCGMGFG.
PhylomeDBiQ9LRM5.

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.

Q9LRM5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATSSLKLTS ACFVLLFIFV GCVLTATNLR NNEISRSRKL KTEDSKSFNS
60 70 80 90 100
SPMTTRLDGV VELNEHAVTD PDKVAHEVSN LIHMSEQNIT ARRKLGFFSC
110 120 130 140 150
GNGNLIDDCW RCDRNWNKNR KHLADCGMGF GSKAFGGRNG SYYVVTDHSD
160 170 180 190 200
DDVVNPKPGT LRHAVIQVEP LWIIFKRDMV IKLKQELIMN SFKTIDARGA
210 220 230 240 250
NVHIANGACI TIQNITNVIV HGLHIHDCKR TGNVTVRSSP SQAGFRGTAD
260 270 280 290 300
GDAINIFGSS HIWIDHNSLS NCTDGLVDVV NGSTAITISN NHFTHHDEVM
310 320 330 340 350
LLGHNDSYTR DKMMQVTVAY NHFGEGLIQR MPRCRHGYFH VVNNDYTHWK
360 370 380 390 400
MYAIGGSANP TINSQGNRFA APKNHSAKEV TKRLDTKGNE WMEWNWRSEK
410 420 430 440 450
DLLVNGAFFT PSGEGASGDS QTLSLPAKPA SMVDAITASA GALSCRRGKP

CY
Length:452
Mass (Da):49,985
Last modified:October 1, 2000 - v1
Checksum:iF31AD9097F923249
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti224 – 2241H → N in BX823056 (PubMed:14993207).Curated
Sequence conflicti306 – 3061D → H in BX823056 (PubMed:14993207).Curated
Sequence conflicti326 – 3261G → A in BX823056 (PubMed:14993207).Curated
Sequence conflicti338 – 3381Y → H in BX823056 (PubMed:14993207).Curated
Sequence conflicti346 – 3461Y → H in BX823056 (PubMed:14993207).Curated
Sequence conflicti408 – 4081F → S in BX823056 (PubMed:14993207).Curated
Sequence conflicti419 – 4191D → H in BX823056 (PubMed:14993207).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB028621 Genomic DNA. Translation: BAB01365.1.
CP002686 Genomic DNA. Translation: AEE76877.1.
BX823056 mRNA. No translation available.
RefSeqiNP_189065.2. NM_113328.2.
UniGeneiAt.50221.

Genome annotation databases

EnsemblPlantsiAT3G24230.1; AT3G24230.1; AT3G24230.
GeneIDi822010.
GrameneiAT3G24230.1; AT3G24230.1; AT3G24230.
KEGGiath:AT3G24230.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB028621 Genomic DNA. Translation: BAB01365.1.
CP002686 Genomic DNA. Translation: AEE76877.1.
BX823056 mRNA. No translation available.
RefSeqiNP_189065.2. NM_113328.2.
UniGeneiAt.50221.

3D structure databases

ProteinModelPortaliQ9LRM5.
SMRiQ9LRM5. Positions 104-414.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT3G24230.1.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Proteomic databases

PaxDbiQ9LRM5.
PRIDEiQ9LRM5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G24230.1; AT3G24230.1; AT3G24230.
GeneIDi822010.
GrameneiAT3G24230.1; AT3G24230.1; AT3G24230.
KEGGiath:AT3G24230.

Organism-specific databases

TAIRiAT3G24230.

Phylogenomic databases

eggNOGiENOG410JSZY. Eukaryota.
COG3866. LUCA.
HOGENOMiHOG000237948.
InParanoidiQ9LRM5.
KOiK01728.
OMAiDCGMGFG.
PhylomeDBiQ9LRM5.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BioCyciARA:AT3G24230-MONOMER.

Miscellaneous databases

PROiQ9LRM5.

Gene expression databases

GenevisibleiQ9LRM5. 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. "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.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Whole genome sequence comparisons and 'full-length' cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation."
    Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M., Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M., Weissenbach J., Salanoubat M.
    Genome Res. 14:406-413(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.

Entry informationi

Entry nameiPLY9_ARATH
AccessioniPrimary (citable) accession number: Q9LRM5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: October 1, 2000
Last modified: May 11, 2016
This is version 105 of the entry and version 1 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.