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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)DescriptionActionsGraphical viewLength
Metal bindingi205Calcium2 Publications1
Metal bindingi244Calcium2 Publications1
Metal bindingi248Calcium2 Publications1
Active sitei3001 Publication1

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 212 PublicationsAdd BLAST21
ChainiPRO_000002485922 – 420Pectate lyaseAdd BLAST399

Proteomic databases

PaxDbiP39116.
PRIDEiP39116.

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

1420
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi24 – 26Combined sources3
Helixi35 – 37Combined sources3
Turni44 – 47Combined sources4
Helixi50 – 52Combined sources3
Beta strandi53 – 56Combined sources4
Helixi59 – 66Combined sources8
Beta strandi75 – 79Combined sources5
Beta strandi81 – 87Combined sources7
Helixi96 – 99Combined sources4
Helixi106 – 113Combined sources8
Helixi115 – 118Combined sources4
Helixi126 – 142Combined sources17
Beta strandi143 – 145Combined sources3
Beta strandi148 – 155Combined sources8
Beta strandi160 – 163Combined sources4
Beta strandi165 – 168Combined sources4
Beta strandi170 – 177Combined sources8
Beta strandi179 – 181Combined sources3
Beta strandi189 – 191Combined sources3
Turni195 – 197Combined sources3
Beta strandi199 – 201Combined sources3
Beta strandi206 – 211Combined sources6
Beta strandi213 – 219Combined sources7
Beta strandi221 – 223Combined sources3
Helixi229 – 231Combined sources3
Beta strandi246 – 250Combined sources5
Beta strandi254 – 260Combined sources7
Beta strandi262 – 268Combined sources7
Beta strandi271 – 273Combined sources3
Helixi279 – 281Combined sources3
Beta strandi287 – 291Combined sources5
Beta strandi293 – 299Combined sources7
Beta strandi301 – 306Combined sources6
Beta strandi308 – 313Combined sources6
Beta strandi315 – 317Combined sources3
Beta strandi323 – 325Combined sources3
Beta strandi330 – 333Combined sources4
Beta strandi338 – 343Combined sources6
Beta strandi345 – 347Combined sources3
Helixi353 – 356Combined sources4
Beta strandi357 – 359Combined sources3
Beta strandi367 – 370Combined sources4
Beta strandi376 – 378Combined sources3
Helixi380 – 383Combined sources4
Helixi403 – 405Combined sources3
Helixi406 – 413Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004223.

Protein family/group databases

CAZyiPL1. Polysaccharide Lyase Family 1.

Proteomic databases

PaxDbiP39116.
PRIDEiP39116.

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: November 2, 2016
This is version 127 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.