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Protein

Pectate lyase

Gene

pel

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Produces unsaturated products from polygalacturonate.

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+1 PublicationNote: Binds 1 Ca2+ ion per subunit.1 Publication

pH dependencei

Optimum pH is 8.4.

Temperature dependencei

Optimum temperature is 42 degrees Celsius.

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. no protein annotated in this organism
  2. Pectate lyase C (pelC), Pectate lyase (pel)
  3. no protein annotated in this organism
  4. 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (kduI)
  5. 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (kduD)
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 bindingi205 – 2051Calcium2 Publications
Metal bindingi244 – 2441Calcium2 Publications
Metal bindingi248 – 2481Calcium2 Publications
Active sitei300 – 30011 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU07560-MONOMER.
BRENDAi4.2.2.2. 658.
UniPathwayiUPA00545; UER00824.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Pectate lyase (EC:4.2.2.2)
Short name:
PL
Gene namesi
Name:pel
Ordered Locus Names:BSU07560
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

  • Secreted 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 21212 PublicationsAdd
BLAST
Chaini22 – 420399Pectate lyasePRO_0000024859Add
BLAST

Proteomic databases

PaxDbiP39116.

Expressioni

Developmental stagei

Produced during the exponential death phase of growth, just before sporulation.

Inductioni

Negatively regulated by TnrA under nitrogen-limited conditions.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004223.

Structurei

Secondary structure

1
420
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi24 – 263Combined sources
Helixi35 – 373Combined sources
Turni44 – 474Combined sources
Helixi50 – 523Combined sources
Beta strandi53 – 564Combined sources
Helixi59 – 668Combined sources
Beta strandi75 – 795Combined sources
Beta strandi81 – 877Combined sources
Helixi96 – 994Combined sources
Helixi106 – 1138Combined sources
Helixi115 – 1184Combined sources
Helixi126 – 14217Combined sources
Beta strandi143 – 1453Combined sources
Beta strandi148 – 1558Combined sources
Beta strandi160 – 1634Combined sources
Beta strandi165 – 1684Combined sources
Beta strandi170 – 1778Combined sources
Beta strandi179 – 1813Combined sources
Beta strandi189 – 1913Combined sources
Turni195 – 1973Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi206 – 2116Combined sources
Beta strandi213 – 2197Combined sources
Beta strandi221 – 2233Combined sources
Helixi229 – 2313Combined sources
Beta strandi246 – 2505Combined sources
Beta strandi254 – 2607Combined sources
Beta strandi262 – 2687Combined sources
Beta strandi271 – 2733Combined sources
Helixi279 – 2813Combined sources
Beta strandi287 – 2915Combined sources
Beta strandi293 – 2997Combined sources
Beta strandi301 – 3066Combined sources
Beta strandi308 – 3136Combined sources
Beta strandi315 – 3173Combined sources
Beta strandi323 – 3253Combined sources
Beta strandi330 – 3334Combined sources
Beta strandi338 – 3436Combined sources
Beta strandi345 – 3473Combined sources
Helixi353 – 3564Combined sources
Beta strandi357 – 3593Combined sources
Beta strandi367 – 3704Combined sources
Beta strandi376 – 3783Combined sources
Helixi380 – 3834Combined sources
Helixi403 – 4053Combined sources
Helixi406 – 4138Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BN8X-ray1.80A1-420[»]
2BSPX-ray1.80A1-420[»]
2NZMX-ray1.80A22-420[»]
2O04X-ray1.70A22-420[»]
2O0VX-ray1.90A22-420[»]
2O0WX-ray1.90A22-420[»]
2O17X-ray2.30A22-420[»]
2O1DX-ray2.00A22-420[»]
3KRGX-ray1.90A22-420[»]
5AMVX-ray1.57A22-420[»]
ProteinModelPortaliP39116.
SMRiP39116. Positions 22-420.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39116.

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 1 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4108J20. Bacteria.
COG3866. LUCA.
HOGENOMiHOG000216909.
InParanoidiP39116.
KOiK01728.
OMAiYLKAYDP.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR002022. Amb_allergen_dom.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00544. Pec_lyase_C. 1 hit.
[Graphical view]
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.

P39116-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKVMLATAL FLGLTPAGAN AADLGHQTLG SNDGWGAYST GTTGGSKASS
60 70 80 90 100
SNVYTVSNRN QLVSALGKET NTTPKIIYIK GTIDMNVDDN LKPLGLNDYK
110 120 130 140 150
DPEYDLDKYL KAYDPSTWGK KEPSGTQEEA RARSQKNQKA RVMVDIPANT
160 170 180 190 200
TIVGSGTNAK VVGGNFQIKS DNVIIRNIEF QDAYDYFPQW DPTDGSSGNW
210 220 230 240 250
NSQYDNITIN GGTHIWIDHC TFNDGSRPDS TSPKYYGRKY QHHDGQTDAS
260 270 280 290 300
NGANYITMSY NYYHDHDKSS IFGSSDSKTS DDGKLKITLH HNRYKNIVQR
310 320 330 340 350
APRVRFGQVH VYNNYYEGST SSSSYPFSYA WGIGKSSKIY AQNNVIDVPG
360 370 380 390 400
LSAAKTISVF SGGTALYDSG TLLNGTQINA SAANGLSSSV GWTPSLHGSI
410 420
DASANVKSNV INQAGAGKLN
Length:420
Mass (Da):45,498
Last modified:February 1, 1995 - v1
Checksum:i6FE93A671B73C15D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74880 Genomic DNA. Translation: CAA52866.1.
D86417 Genomic DNA. Translation: BAA22313.1.
AL009126 Genomic DNA. Translation: CAB12585.1.
PIRiS39459.
RefSeqiNP_388637.1. NC_000964.3.
WP_003244025.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12585; CAB12585; BSU07560.
GeneIDi936113.
KEGGibsu:BSU07560.
PATRICi18973162. VBIBacSub10457_0795.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74880 Genomic DNA. Translation: CAA52866.1.
D86417 Genomic DNA. Translation: BAA22313.1.
AL009126 Genomic DNA. Translation: CAB12585.1.
PIRiS39459.
RefSeqiNP_388637.1. NC_000964.3.
WP_003244025.1. NZ_JNCM01000032.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BN8X-ray1.80A1-420[»]
2BSPX-ray1.80A1-420[»]
2NZMX-ray1.80A22-420[»]
2O04X-ray1.70A22-420[»]
2O0VX-ray1.90A22-420[»]
2O0WX-ray1.90A22-420[»]
2O17X-ray2.30A22-420[»]
2O1DX-ray2.00A22-420[»]
3KRGX-ray1.90A22-420[»]
5AMVX-ray1.57A22-420[»]
ProteinModelPortaliP39116.
SMRiP39116. Positions 22-420.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004223.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Proteomic databases

PaxDbiP39116.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12585; CAB12585; BSU07560.
GeneIDi936113.
KEGGibsu:BSU07560.
PATRICi18973162. VBIBacSub10457_0795.

Phylogenomic databases

eggNOGiENOG4108J20. Bacteria.
COG3866. LUCA.
HOGENOMiHOG000216909.
InParanoidiP39116.
KOiK01728.
OMAiYLKAYDP.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00824.
BioCyciBSUB:BSU07560-MONOMER.
BRENDAi4.2.2.2. 658.

Miscellaneous databases

EvolutionaryTraceiP39116.

Family and domain databases

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

Entry informationi

Entry nameiPLY_BACSU
AccessioniPrimary (citable) accession number: P39116
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.