UniProtKB - P39130 (LPLD_BACSU)
Alpha-galacturonidase
lplD
Functioni
Alpha-galacturonidase able to catalyze the hydrolysis of the chromogenic substrate p-nitrophenyl-alpha-D-galacturonic acid (pNPalphaGalUA), and of the probable natural substrate alpha-1,4-di-galacturonate (GalUA2). Can neither hydrolyze pNPbetaGalUA, nor the stereoisomeric pNPalphaGlcUA. Does not display alpha- or beta-glucosidase activity as it fails to hydrolyze melibiose, raffinose, lactose and the chromogenic analogs, pNPalphaGal and pNPbetaGal. Cannot use the following compounds as substrates: pNP-N-acetyl-alpha- and beta-D-galactosaminide, pNP-N-acetyl-alpha- and beta-D-glucosaminide, pNP-alpha-L- and beta-L-arabinopyranoside, pNP-alpha- and beta-D-glucuronide, pNP-alpha- and beta-D-glucopyranoside, pNP-alpha- and beta-D-glucopyranoside 6-phosphate, pNP-alpha-D-galactopyranoside 6-phosphate and oNP-beta-D-galactopyranoside 6-phosphate.
1 PublicationCatalytic activityi
- [(1→4)-α-D-galacturonosyl](n) + H2O = [(1→4)-α-D-galacturonosyl](n-1) + α-D-galacturonate1 PublicationEC:3.2.1.671 Publication
Cofactori
Protein has several cofactor binding sites:- NAD+1 Publication
- Mn2+1 PublicationNote: Binds 1 Mn2+ ion per subunit. Although a Mg2+ ion is seen in the structure, galacturonidase activity was shown using manganese (PubMed:23416295).1 Publication
Kineticsi
- KM=0.62 µM for pNPalphaGalUA (at about 37 degrees Celsius)1 Publication
- Vmax=4.33 µmol/min/mg enzyme with pNPalphaGalUA as substrate (at about 37 degrees Celsius)1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 151 | SubstrateBy similarity | 1 | |
Metal bindingi | 173 | Manganese | 1 | |
Active sitei | 174 | Proton donorBy similarity | 1 | |
Metal bindingi | 210 | Manganese | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 10 – 72 | NADBy similarityAdd BLAST | 63 |
GO - Molecular functioni
- galacturan 1,4-alpha-galacturonidase activity Source: UniProtKB-EC
- metal ion binding Source: UniProtKB-KW
- oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Source: InterPro
GO - Biological processi
- carbohydrate metabolic process Source: UniProtKB-KW
Keywordsi
Molecular function | Glycosidase, Hydrolase |
Biological process | Carbohydrate metabolism |
Ligand | Manganese, Metal-binding, NAD |
Enzyme and pathway databases
BioCyci | BSUB:BSU07130-MONOMER |
Protein family/group databases
CAZyi | GH4, Glycoside Hydrolase Family 4 |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:lplD Ordered Locus Names:BSU07130 |
Organismi | Bacillus subtilis (strain 168) |
Taxonomic identifieri | 224308 [NCBI] |
Taxonomic lineagei | Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 172 | C → L: Does not significantly affect alpha-galacturonidase activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000169862 | 1 – 446 | Alpha-galacturonidaseAdd BLAST | 446 |
Proteomic databases
PaxDbi | P39130 |
PRIDEi | P39130 |
Interactioni
Subunit structurei
Homotetramer.
2 PublicationsProtein-protein interaction databases
STRINGi | 224308.BSU07130 |
Structurei
Secondary structure
3D structure databases
SMRi | P39130 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P39130 |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG1486, Bacteria |
InParanoidi | P39130 |
OMAi | EMYSDVH |
PhylomeDBi | P39130 |
Family and domain databases
InterProi | View protein in InterPro IPR019802, GlycHydrolase_4_CS IPR001088, Glyco_hydro_4 IPR022616, Glyco_hydro_4_C IPR015955, Lactate_DH/Glyco_Ohase_4_C IPR036291, NAD(P)-bd_dom_sf |
PANTHERi | PTHR32092, PTHR32092, 1 hit |
Pfami | View protein in Pfam PF02056, Glyco_hydro_4, 1 hit PF11975, Glyco_hydro_4C, 1 hit |
PRINTSi | PR00732, GLHYDRLASE4 |
SUPFAMi | SSF51735, SSF51735, 1 hit SSF56327, SSF56327, 1 hit |
PROSITEi | View protein in PROSITE PS01324, GLYCOSYL_HYDROL_F4, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MFHISTLDQI KIAYIGGGSQ GWARSLMSDL SIDERMSGTV ALYDLDFEAA
60 70 80 90 100
QKNEVIGNHS GNGRWRYEAV STLKKALSAA DIVIISILPG SLDDMEVDVH
110 120 130 140 150
LPERCGIYQS VGDTVGPGGI IRGLRAVPIF AEIARAIRDY APESWVINYT
160 170 180 190 200
NPMSVCTRVL YKVFPGIKAI GCCHEVFGTQ KLLAEMVTER LGIEVPRRED
210 220 230 240 250
IRVNVLGINH FTWITKASYR HIDLLPIFRE FSAHYGESGY ELEGECWRDS
260 270 280 290 300
VFCSAHRVAF DLFETYGAIP AAGDRHLAEF LPGPYLKQPE VWKFHLTPIS
310 320 330 340 350
FRKQDRAEKR QETERLIVQQ RGVAEKASGE EGVNIIAALL GLGELVTNVN
360 370 380 390 400
MPNQGQVLNL PIQAIVETNA FITRNRVQPI LSGALPKGVE MLAARHISNQ
410 420 430 440
EAVADAGLTK DTGLAFQAFL NDPLVQIDRS DAEQLFNDML QCIMQS
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 66 | R → T in AAA22577 (Ref. 1) Curated | 1 | |
Sequence conflicti | 154 | S → Y in AAA22577 (Ref. 1) Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L19165 Genomic DNA Translation: AAA22577.1 AL009126 Genomic DNA Translation: CAB12532.1 |
PIRi | C69653 |
RefSeqi | NP_388594.1, NC_000964.3 WP_003244472.1, NZ_JNCM01000032.1 |
Genome annotation databases
EnsemblBacteriai | CAB12532; CAB12532; BSU_07130 |
GeneIDi | 938770 |
KEGGi | bsu:BSU07130 |
PATRICi | fig|224308.179.peg.773 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L19165 Genomic DNA Translation: AAA22577.1 AL009126 Genomic DNA Translation: CAB12532.1 |
PIRi | C69653 |
RefSeqi | NP_388594.1, NC_000964.3 WP_003244472.1, NZ_JNCM01000032.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3FEF | X-ray | 2.20 | A/B/C/D | 7-446 | [»] | |
SMRi | P39130 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 224308.BSU07130 |
Protein family/group databases
CAZyi | GH4, Glycoside Hydrolase Family 4 |
Proteomic databases
PaxDbi | P39130 |
PRIDEi | P39130 |
Protocols and materials databases
DNASUi | 938770 |
Genome annotation databases
EnsemblBacteriai | CAB12532; CAB12532; BSU_07130 |
GeneIDi | 938770 |
KEGGi | bsu:BSU07130 |
PATRICi | fig|224308.179.peg.773 |
Phylogenomic databases
eggNOGi | COG1486, Bacteria |
InParanoidi | P39130 |
OMAi | EMYSDVH |
PhylomeDBi | P39130 |
Enzyme and pathway databases
BioCyci | BSUB:BSU07130-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P39130 |
Family and domain databases
InterProi | View protein in InterPro IPR019802, GlycHydrolase_4_CS IPR001088, Glyco_hydro_4 IPR022616, Glyco_hydro_4_C IPR015955, Lactate_DH/Glyco_Ohase_4_C IPR036291, NAD(P)-bd_dom_sf |
PANTHERi | PTHR32092, PTHR32092, 1 hit |
Pfami | View protein in Pfam PF02056, Glyco_hydro_4, 1 hit PF11975, Glyco_hydro_4C, 1 hit |
PRINTSi | PR00732, GLHYDRLASE4 |
SUPFAMi | SSF51735, SSF51735, 1 hit SSF56327, SSF56327, 1 hit |
PROSITEi | View protein in PROSITE PS01324, GLYCOSYL_HYDROL_F4, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | LPLD_BACSU | |
Accessioni | P39130Primary (citable) accession number: P39130 Secondary accession number(s): O31532 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | February 1, 1995 |
Last sequence update: | December 15, 1998 | |
Last modified: | September 29, 2021 | |
This is version 134 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Glycosyl hydrolases
Classification of glycosyl hydrolase families and list of entries - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families