LPLD_BACSU
ID LPLD_BACSU Reviewed; 446 AA.
AC P39130; O31532;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-1998, sequence version 2.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Alpha-galacturonidase;
DE EC=3.2.1.67;
GN Name=lplD; OrderedLocusNames=BSU07130;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RA Gomez A., Ramon D., Sanz P.;
RT "The complete lpl cluster of Bacillus subtilis.";
RL Submitted (JAN-1994) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, KINETIC
RP PARAMETERS, SUBUNIT, AND MUTAGENESIS OF CYS-172.
RC STRAIN=168;
RX PubMed=23416295; DOI=10.1016/j.febslet.2013.02.004;
RA Thompson J., Pikis A., Rich J., Hall B.G., Withers S.G.;
RT "alpha-Galacturonidase(s): A new class of Family 4 glycoside hydrolases
RT with strict specificity and a unique CHEV active site motif.";
RL FEBS Lett. 587:799-803(2013).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 7-446 IN COMPLEX WITH MAGNESIUM,
RP AND SUBUNIT.
RG New York SGX Research Center for Structural Genomics (NYSGXRC);
RT "Crystal structure of putative glucosidase LplD from Bacillus subtilis.";
RL Submitted (DEC-2008) to the PDB data bank.
CC -!- FUNCTION: Alpha-galacturonidase able to catalyze the hydrolysis of the
CC chromogenic substrate p-nitrophenyl-alpha-D-galacturonic acid
CC (pNPalphaGalUA), and of the probable natural substrate alpha-1,4-di-
CC galacturonate (GalUA(2)). Can neither hydrolyze pNPbetaGalUA, nor the
CC stereoisomeric pNPalphaGlcUA. Does not display alpha- or beta-
CC glucosidase activity as it fails to hydrolyze melibiose, raffinose,
CC lactose and the chromogenic analogs, pNPalphaGal and pNPbetaGal. Cannot
CC use the following compounds as substrates: pNP-N-acetyl-alpha- and
CC beta-D-galactosaminide, pNP-N-acetyl-alpha- and beta-D-glucosaminide,
CC pNP-alpha-L- and beta-L-arabinopyranoside, pNP-alpha- and beta-D-
CC glucuronide, pNP-alpha- and beta-D-glucopyranoside, pNP-alpha- and
CC beta-D-glucopyranoside 6-phosphate, pNP-alpha-D-galactopyranoside 6-
CC phosphate and oNP-beta-D-galactopyranoside 6-phosphate.
CC {ECO:0000269|PubMed:23416295}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[(1->4)-alpha-D-galacturonosyl](n) + H2O = [(1->4)-alpha-D-
CC galacturonosyl](n-1) + alpha-D-galacturonate; Xref=Rhea:RHEA:14117,
CC Rhea:RHEA-COMP:14570, Rhea:RHEA-COMP:14572, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:58658, ChEBI:CHEBI:140523; EC=3.2.1.67;
CC Evidence={ECO:0000269|PubMed:23416295};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000305|PubMed:23416295};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23416295};
CC Note=Binds 1 Mn(2+) ion per subunit. Although a Mg(2+) ion is seen in
CC the structure, galacturonidase activity was shown using manganese
CC (PubMed:23416295). {ECO:0000269|PubMed:23416295};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.62 uM for pNPalphaGalUA (at about 37 degrees Celsius)
CC {ECO:0000269|PubMed:23416295};
CC Vmax=4.33 umol/min/mg enzyme with pNPalphaGalUA as substrate (at
CC about 37 degrees Celsius) {ECO:0000269|PubMed:23416295};
CC Note=kcat is 3.6 sec(-1) with pNPalphaGalUA as substrate (at about 37
CC degrees Celsius).;
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:23416295,
CC ECO:0000269|Ref.4}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 4 family. {ECO:0000305}.
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DR EMBL; L19165; AAA22577.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12532.1; -; Genomic_DNA.
DR PIR; C69653; C69653.
DR RefSeq; NP_388594.1; NC_000964.3.
DR RefSeq; WP_003244472.1; NZ_JNCM01000032.1.
DR PDB; 3FEF; X-ray; 2.20 A; A/B/C/D=7-446.
DR PDBsum; 3FEF; -.
DR AlphaFoldDB; P39130; -.
DR SMR; P39130; -.
DR STRING; 224308.BSU07130; -.
DR CAZy; GH4; Glycoside Hydrolase Family 4.
DR PaxDb; P39130; -.
DR PRIDE; P39130; -.
DR DNASU; 938770; -.
DR EnsemblBacteria; CAB12532; CAB12532; BSU_07130.
DR GeneID; 938770; -.
DR KEGG; bsu:BSU07130; -.
DR PATRIC; fig|224308.179.peg.773; -.
DR eggNOG; COG1486; Bacteria.
DR InParanoid; P39130; -.
DR OMA; EMYSDVH; -.
DR PhylomeDB; P39130; -.
DR BioCyc; BSUB:BSU07130-MON; -.
DR EvolutionaryTrace; P39130; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0047911; F:galacturan 1,4-alpha-galacturonidase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016616; F:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor; IEA:InterPro.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR InterPro; IPR019802; GlycHydrolase_4_CS.
DR InterPro; IPR001088; Glyco_hydro_4.
DR InterPro; IPR022616; Glyco_hydro_4_C.
DR InterPro; IPR015955; Lactate_DH/Glyco_Ohase_4_C.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR32092; PTHR32092; 1.
DR Pfam; PF02056; Glyco_hydro_4; 1.
DR Pfam; PF11975; Glyco_hydro_4C; 1.
DR PRINTS; PR00732; GLHYDRLASE4.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF56327; SSF56327; 1.
DR PROSITE; PS01324; GLYCOSYL_HYDROL_F4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Glycosidase; Hydrolase; Manganese;
KW Metal-binding; NAD; Reference proteome.
FT CHAIN 1..446
FT /note="Alpha-galacturonidase"
FT /id="PRO_0000169862"
FT ACT_SITE 174
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 10..72
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 151
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 173
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT BINDING 210
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT MUTAGEN 172
FT /note="C->L: Does not significantly affect alpha-
FT galacturonidase activity."
FT /evidence="ECO:0000269|PubMed:23416295"
FT CONFLICT 66
FT /note="R -> T (in Ref. 1; AAA22577)"
FT /evidence="ECO:0000305"
FT CONFLICT 154
FT /note="S -> Y (in Ref. 1; AAA22577)"
FT /evidence="ECO:0000305"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:3FEF"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 22..32
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 47..57
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 73..77
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 92..100
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 101..105
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 116..140
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 153..163
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 168..171
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 175..191
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 201..208
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 211..219
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 224..235
FT /evidence="ECO:0007829|PDB:3FEF"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 257..266
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 267..270
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 274..277
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 285..287
FT /evidence="ECO:0007829|PDB:3FEF"
FT TURN 289..293
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 299..318
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 332..339
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 345..352
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 354..357
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 364..373
FT /evidence="ECO:0007829|PDB:3FEF"
FT STRAND 376..380
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 387..409
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 412..421
FT /evidence="ECO:0007829|PDB:3FEF"
FT HELIX 429..439
FT /evidence="ECO:0007829|PDB:3FEF"
SQ SEQUENCE 446 AA; 49487 MW; 691FEC5C371B9F5B CRC64;
MFHISTLDQI KIAYIGGGSQ GWARSLMSDL SIDERMSGTV ALYDLDFEAA QKNEVIGNHS
GNGRWRYEAV STLKKALSAA DIVIISILPG SLDDMEVDVH LPERCGIYQS VGDTVGPGGI
IRGLRAVPIF AEIARAIRDY APESWVINYT NPMSVCTRVL YKVFPGIKAI GCCHEVFGTQ
KLLAEMVTER LGIEVPRRED IRVNVLGINH FTWITKASYR HIDLLPIFRE FSAHYGESGY
ELEGECWRDS VFCSAHRVAF DLFETYGAIP AAGDRHLAEF LPGPYLKQPE VWKFHLTPIS
FRKQDRAEKR QETERLIVQQ RGVAEKASGE EGVNIIAALL GLGELVTNVN MPNQGQVLNL
PIQAIVETNA FITRNRVQPI LSGALPKGVE MLAARHISNQ EAVADAGLTK DTGLAFQAFL
NDPLVQIDRS DAEQLFNDML QCIMQS
