PLY_BACSU
ID PLY_BACSU Reviewed; 420 AA.
AC P39116;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Pectate lyase;
DE Short=PL;
DE EC=4.2.2.2;
DE Flags: Precursor;
GN Name=pel; OrderedLocusNames=BSU07560;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 22-48.
RC STRAIN=168 / SO113;
RX PubMed=8262178; DOI=10.1016/0014-5793(93)80410-v;
RA Nasser W., Awade A.C., Reverchon S., Robert-Baudouy J.;
RT "Pectate lyase from Bacillus subtilis: molecular characterization of the
RT gene, and properties of the cloned enzyme.";
RL FEBS Lett. 335:319-326(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / AC327;
RX PubMed=9272861; DOI=10.1016/s0378-1119(97)00130-3;
RA Yamamoto H., Uchiyama S., Nugroho F.A., Sekiguchi J.;
RT "Cloning and sequencing of a 35.7 kb in the 70 degree-73 degree region of
RT the Bacillus subtilis genome reveal genes for a new two-component system,
RT three spore germination proteins, an iron uptake system and a general
RT stress response protein.";
RL Gene 194:191-199(1997).
RN [3]
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 [4]
RP PROTEIN SEQUENCE OF 22-32, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=10658653; DOI=10.1099/00221287-146-1-65;
RA Hirose I., Sano K., Shioda I., Kumano M., Nakamura K., Yamane K.;
RT "Proteome analysis of Bacillus subtilis extracellular proteins: a two-
RT dimensional protein electrophoretic study.";
RL Microbiology 146:65-75(2000).
RN [5]
RP CHARACTERIZATION.
RC STRAIN=168 / SO113;
RX PubMed=2126210; DOI=10.1016/0300-9084(90)90053-j;
RA Nasser W., Chalet F., Robert-Baudouy J.;
RT "Purification and characterization of extracellular pectate lyase from
RT Bacillus subtilis.";
RL Biochimie 72:689-695(1990).
RN [6]
RP REGULATION BY TNRA.
RX PubMed=12823818; DOI=10.1046/j.1365-2958.2003.03567.x;
RA Yoshida K., Yamaguchi H., Kinehara M., Ohki Y.-H., Nakaura Y., Fujita Y.;
RT "Identification of additional TnrA-regulated genes of Bacillus subtilis
RT associated with a TnrA box.";
RL Mol. Microbiol. 49:157-165(2003).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CALCIUM.
RX PubMed=7634076; DOI=10.1038/nsb1094-717;
RA Pickersgill R., Jenkins J., Harris G., Nasser W., Robert-Baudouy J.;
RT "The structure of Bacillus subtilis pectate lyase in complex with
RT calcium.";
RL Nat. Struct. Biol. 1:717-723(1994).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH CALCIUM.
RA Pickersgill R., Worboys K., Scott M., Cummings N., Cooper A., Jenkins J.,
RA Smith D.;
RL Submitted (JUL-1998) to the PDB data bank.
CC -!- FUNCTION: Produces unsaturated products from polygalacturonate.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Eliminative cleavage of (1->4)-alpha-D-galacturonan to give
CC oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at
CC their non-reducing ends.; EC=4.2.2.2;
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:7634076};
CC Note=Binds 1 Ca(2+) ion per subunit. {ECO:0000269|PubMed:7634076};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.4.;
CC Temperature dependence:
CC Optimum temperature is 42 degrees Celsius.;
CC -!- PATHWAY: Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-
CC gluconate from pectin: step 2/5.
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:10658653}.
CC -!- DEVELOPMENTAL STAGE: Produced during the exponential death phase of
CC growth, just before sporulation.
CC -!- INDUCTION: Negatively regulated by TnrA under nitrogen-limited
CC conditions.
CC -!- SIMILARITY: Belongs to the polysaccharide lyase 1 family.
CC {ECO:0000305}.
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DR EMBL; X74880; CAA52866.1; -; Genomic_DNA.
DR EMBL; D86417; BAA22313.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12585.1; -; Genomic_DNA.
DR PIR; S39459; S39459.
DR RefSeq; NP_388637.1; NC_000964.3.
DR RefSeq; WP_003244025.1; NZ_JNCM01000032.1.
DR PDB; 1BN8; X-ray; 1.80 A; A=1-420.
DR PDB; 2BSP; X-ray; 1.80 A; A=1-420.
DR PDB; 2NZM; X-ray; 1.80 A; A=22-420.
DR PDB; 2O04; X-ray; 1.70 A; A=22-420.
DR PDB; 2O0V; X-ray; 1.90 A; A=22-420.
DR PDB; 2O0W; X-ray; 1.90 A; A=22-420.
DR PDB; 2O17; X-ray; 2.30 A; A=22-420.
DR PDB; 2O1D; X-ray; 2.00 A; A=22-420.
DR PDB; 3KRG; X-ray; 1.90 A; A=22-420.
DR PDB; 5AMV; X-ray; 1.57 A; A=22-420.
DR PDB; 5X2I; X-ray; 2.05 A; A=22-420.
DR PDBsum; 1BN8; -.
DR PDBsum; 2BSP; -.
DR PDBsum; 2NZM; -.
DR PDBsum; 2O04; -.
DR PDBsum; 2O0V; -.
DR PDBsum; 2O0W; -.
DR PDBsum; 2O17; -.
DR PDBsum; 2O1D; -.
DR PDBsum; 3KRG; -.
DR PDBsum; 5AMV; -.
DR PDBsum; 5X2I; -.
DR AlphaFoldDB; P39116; -.
DR SMR; P39116; -.
DR STRING; 224308.BSU07560; -.
DR CAZy; PL1; Polysaccharide Lyase Family 1.
DR PaxDb; P39116; -.
DR PRIDE; P39116; -.
DR EnsemblBacteria; CAB12585; CAB12585; BSU_07560.
DR GeneID; 936113; -.
DR KEGG; bsu:BSU07560; -.
DR PATRIC; fig|224308.179.peg.821; -.
DR eggNOG; COG3866; Bacteria.
DR InParanoid; P39116; -.
DR OMA; GNWNSQY; -.
DR BioCyc; BSUB:BSU07560-MON; -.
DR BRENDA; 4.2.2.2; 658.
DR UniPathway; UPA00545; UER00824.
DR EvolutionaryTrace; P39116; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030570; F:pectate lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0045490; P:pectin catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.160.20.10; -; 1.
DR InterPro; IPR002022; Pec_lyase.
DR InterPro; IPR012334; Pectin_lyas_fold.
DR InterPro; IPR011050; Pectin_lyase_fold/virulence.
DR InterPro; IPR045032; PEL.
DR PANTHER; PTHR31683; PTHR31683; 1.
DR Pfam; PF00544; Pectate_lyase_4; 1.
DR SMART; SM00656; Amb_all; 1.
DR SUPFAM; SSF51126; SSF51126; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Direct protein sequencing; Lyase; Metal-binding;
KW Reference proteome; Secreted; Signal.
FT SIGNAL 1..21
FT /evidence="ECO:0000269|PubMed:10658653,
FT ECO:0000269|PubMed:8262178"
FT CHAIN 22..420
FT /note="Pectate lyase"
FT /id="PRO_0000024859"
FT REGION 117..139
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 124..138
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 300
FT /evidence="ECO:0000305|PubMed:7634076"
FT BINDING 205
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:7634076, ECO:0000269|Ref.8"
FT BINDING 244
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:7634076, ECO:0000269|Ref.8"
FT BINDING 248
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:7634076, ECO:0000269|Ref.8"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:5AMV"
FT TURN 44..47
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 53..56
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 96..99
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 106..113
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 115..118
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 126..142
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:5AMV"
FT TURN 195..197
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 206..211
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 213..219
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 246..250
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 262..268
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:2O04"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 287..291
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 293..299
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 301..306
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 308..313
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 323..325
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 330..333
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 338..343
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 353..356
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 367..370
FT /evidence="ECO:0007829|PDB:5AMV"
FT STRAND 376..378
FT /evidence="ECO:0007829|PDB:2O1D"
FT HELIX 380..383
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:5AMV"
FT HELIX 406..413
FT /evidence="ECO:0007829|PDB:5AMV"
SQ SEQUENCE 420 AA; 45498 MW; 6FE93A671B73C15D CRC64;
MKKVMLATAL FLGLTPAGAN AADLGHQTLG SNDGWGAYST GTTGGSKASS SNVYTVSNRN
QLVSALGKET NTTPKIIYIK GTIDMNVDDN LKPLGLNDYK DPEYDLDKYL KAYDPSTWGK
KEPSGTQEEA RARSQKNQKA RVMVDIPANT TIVGSGTNAK VVGGNFQIKS DNVIIRNIEF
QDAYDYFPQW DPTDGSSGNW NSQYDNITIN GGTHIWIDHC TFNDGSRPDS TSPKYYGRKY
QHHDGQTDAS NGANYITMSY NYYHDHDKSS IFGSSDSKTS DDGKLKITLH HNRYKNIVQR
APRVRFGQVH VYNNYYEGST SSSSYPFSYA WGIGKSSKIY AQNNVIDVPG LSAAKTISVF
SGGTALYDSG TLLNGTQINA SAANGLSSSV GWTPSLHGSI DASANVKSNV INQAGAGKLN
