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UniProtKB - P39130 (LPLD_BACSU)

Entry version 128 (11 Dec 2019)
Sequence version 2 (15 Dec 1998)
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Protein

Alpha-galacturonidase

Gene

lplD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 3.6 sec(-1) with pNPalphaGalUA as substrate (at about 37 degrees Celsius).
  1. KM=0.62 µM for pNPalphaGalUA (at about 37 degrees Celsius)1 Publication
  1. Vmax=4.33 µmol/min/mg enzyme with pNPalphaGalUA as substrate (at about 37 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei151SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi173Manganese1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei174Proton donorBy similarity1
Metal bindingi210Manganese1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi10 – 72NADBy similarityAdd BLAST63

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionGlycosidase, Hydrolase
Biological processCarbohydrate metabolism
LigandManganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU07130-MONOMER

Protein family/group databases

Carbohydrate-Active enZymes

More...CAZyi		GH4 Glycoside Hydrolase Family 4

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Alpha-galacturonidase (EC:3.2.1.67)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:lplD
Ordered Locus Names:BSU07130
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi172C → L: Does not significantly affect alpha-galacturonidase activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001698621 – 446Alpha-galacturonidaseAdd BLAST446

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P39130

PRoteomics IDEntifications database

More...PRIDEi		P39130

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.

2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		224308.BSU07130

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1446
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P39130

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P39130

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the glycosyl hydrolase 4 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105F8D Bacteria
COG1486 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000270081

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P39130

KEGG Orthology (KO)

More...KOi		K22933

Identification of Orthologs from Complete Genome Data

More...OMAi		EMYSDVH

Database for complete collections of gene phylogenies

More...PhylomeDBi		P39130

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...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

The PANTHER Classification System

More...PANTHERi		PTHR32092 PTHR32092, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02056 Glyco_hydro_4, 1 hit
PF11975 Glyco_hydro_4C, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00732 GLHYDRLASE4

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51735 SSF51735, 1 hit
SSF56327 SSF56327, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01324 GLYCOSYL_HYDROL_F4, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P39130-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:446
Mass (Da):49,487
Last modified:December 15, 1998 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i691FEC5C371B9F5B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti66R → T in AAA22577 (Ref. 1) Curated1
Sequence conflicti154S → Y in AAA22577 (Ref. 1) Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L19165 Genomic DNA Translation: AAA22577.1
AL009126 Genomic DNA Translation: CAB12532.1

Protein sequence database of the Protein Information Resource

More...PIRi		C69653

NCBI Reference Sequences

More...RefSeqi		NP_388594.1, NC_000964.3
WP_003244472.1, NZ_JNCM01000032.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB12532; CAB12532; BSU07130

Database of genes from NCBI RefSeq genomes

More...GeneIDi		938770

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU07130

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.773

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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
PIRiC69653
RefSeqiNP_388594.1, NC_000964.3
WP_003244472.1, NZ_JNCM01000032.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3FEFX-ray2.20A/B/C/D7-446[»]
SMRiP39130
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU07130

Protein family/group databases

CAZyiGH4 Glycoside Hydrolase Family 4

Proteomic databases

PaxDbiP39130
PRIDEiP39130

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		938770

Genome annotation databases

EnsemblBacteriaiCAB12532; CAB12532; BSU07130
GeneIDi938770
KEGGibsu:BSU07130
PATRICifig|224308.179.peg.773

Phylogenomic databases

eggNOGiENOG4105F8D Bacteria
COG1486 LUCA
HOGENOMiHOG000270081
InParanoidiP39130
KOiK22933
OMAiEMYSDVH
PhylomeDBiP39130

Enzyme and pathway databases

BioCyciBSUB:BSU07130-MONOMER

Miscellaneous databases

EvolutionaryTraceiP39130

Family and domain databases

InterProiView 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
PANTHERiPTHR32092 PTHR32092, 1 hit
PfamiView protein in Pfam
PF02056 Glyco_hydro_4, 1 hit
PF11975 Glyco_hydro_4C, 1 hit
PRINTSiPR00732 GLHYDRLASE4
SUPFAMiSSF51735 SSF51735, 1 hit
SSF56327 SSF56327, 1 hit
PROSITEiView protein in PROSITE
PS01324 GLYCOSYL_HYDROL_F4, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLPLD_BACSU
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P39130
Secondary accession number(s): O31532
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 15, 1998
Last modified: December 11, 2019
This is version 128 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
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