Pectate lyase precursor - Bacillus subtilis

Names and origin

Protein names

Recommended name:
    Pectate lyase
      Short name=PL
    EC=4.2.2.2

Gene names

Name:	pel
Ordered Locus Names:	BSU07560

Organism

Bacillus subtilis [Complete proteome] [HAMAP]

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

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Protein attributes

Sequence length	420 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Produces unsaturated products from polygalacturonate.
Catalytic activity	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.
Cofactor	Binds 1 calcium ion per subunit.
Pathway	Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconic acid from pectin: step 2/5.
Subunit structure	Monomer.
Subcellular location	Secreted. Ref.4
Developmental stage	Produced during the exponential death phase of growth, just before sporulation.
Sequence similarities	Belongs to the polysaccharide lyase 1 family.
biophysicochemical properties	pH dependence: Optimum pH is 8.4. Temperature dependence: Optimum temperature is 42 degrees Celsius.

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Ontologies

Keywords
Cellular component	Secreted
Domain	Signal
Ligand	Calcium Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Cellular component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW pectate lyase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 21

21

Ref.4 Ref.1

Chain

22 – 420

399

Pectate lyase

PRO_0000024859

Sites

Active site

300

1

Potential

Metal binding

205

1

Calcium

Metal binding

244

1

Calcium

Metal binding

248

1

Calcium

Secondary structure

1

.

420

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P39116-1 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 6FE93A671B73C15D
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FASTA

420

45,498

        10         20         30         40         50         60 
MKKVMLATAL FLGLTPAGAN AADLGHQTLG SNDGWGAYST GTTGGSKASS SNVYTVSNRN 

        70         80         90        100        110        120 
QLVSALGKET NTTPKIIYIK GTIDMNVDDN LKPLGLNDYK DPEYDLDKYL KAYDPSTWGK 

       130        140        150        160        170        180 
KEPSGTQEEA RARSQKNQKA RVMVDIPANT TIVGSGTNAK VVGGNFQIKS DNVIIRNIEF 

       190        200        210        220        230        240 
QDAYDYFPQW DPTDGSSGNW NSQYDNITIN GGTHIWIDHC TFNDGSRPDS TSPKYYGRKY 

       250        260        270        280        290        300 
QHHDGQTDAS NGANYITMSY NYYHDHDKSS IFGSSDSKTS DDGKLKITLH HNRYKNIVQR 

       310        320        330        340        350        360 
APRVRFGQVH VYNNYYEGST SSSSYPFSYA WGIGKSSKIY AQNNVIDVPG LSAAKTISVF 

       370        380        390        400        410        420 
SGGTALYDSG TLLNGTQINA SAANGLSSSV GWTPSLHGSI DASANVKSNV INQAGAGKLN

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Pectate lyase from Bacillus subtilis: molecular characterization of the gene, and properties of the cloned enzyme." Nasser W., Awade A.C., Reverchon S., Robert-Baudouy J. FEBS Lett. 335:319-326(1993) [PubMed: 8262178] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 22-48. Strain: 168 / SO113.
[2]	"Cloning and sequencing of a 35.7 kb in the 70 degree-73 degree region of the Bacillus subtilis genome reveal genes for a new two-component system, three spore germination proteins, an iron uptake system and a general stress response protein." Yamamoto H., Uchiyama S., Nugroho F.A., Sekiguchi J. Gene 194:191-199(1997) [PubMed: 9272861] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / AC327.
[3]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. Danchin A. Nature 390:249-256(1997) [PubMed: 9384377] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[4]	"Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study." Hirose I., Sano K., Shioda I., Kumano M., Nakamura K., Yamane K. Microbiology 146:65-75(2000) [PubMed: 10658653] [Abstract] Cited for: PROTEIN SEQUENCE OF 22-32, SUBCELLULAR LOCATION. Strain: 168.
[5]	"Purification and characterization of extracellular pectate lyase from Bacillus subtilis." Nasser W., Chalet F., Robert-Baudouy J. Biochimie 72:689-695(1990) [PubMed: 2126210] [Abstract] Cited for: CHARACTERIZATION. Strain: 168 / SO113.
[6]	"The structure of Bacillus subtilis pectate lyase in complex with calcium." Pickersgill R., Jenkins J., Harris G., Nasser W., Robert-Baudouy J. Nat. Struct. Biol. 1:717-723(1994) [PubMed: 7634076] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[7]	Pickersgill R., Worboys K., Scott M., Cummings N., Cooper A., Jenkins J., Smith D. Submitted (JUL-1998) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

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Cross-references

Sequence databases

X74880 Genomic DNA. Translation: CAA52866.1.
D86417 Genomic DNA. Translation: BAA22313.1.
AL009126 Genomic DNA. Translation: CAB12585.1.

PIR

S39459.

RefSeq

NP_388637.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BN8	X-ray	1.80	A	1-420	[»]
2BSP	X-ray	1.80	A	1-420	[»]
2NZM	X-ray	1.80	A	22-420	[»]
2O04	X-ray	1.70	A	22-420	[»]
2O0V	X-ray	1.90	A	22-420	[»]
2O0W	X-ray	1.90	A	22-420	[»]
2O17	X-ray	2.30	A	22-420	[»]
2O1D	X-ray	2.00	A	22-420	[»]

ModBase

Search...

Protein family/group databases

CAZy

PL1. Polysaccharide Lyase Family 1.

Genome annotation databases

GeneID

936113.

GenomeReviews

Gene locus BSU07560 in contig AL009126_GR.

KEGG

bsu:BSU07560.

NMPDR

fig|224308.1.peg.756.

Organism-specific databases

SubtiList

BG10840. pel. [Micado]

CMR

Search...

Phylogenomic databases

HOGENOM

P39116.

OMA

P39116. NTTIIGL.

Enzyme and pathway databases

BioCyc

BSUB224308:BSU0756-MON.

BRENDA

4.2.2.2. 150.

Family and domain databases

InterPro

IPR002022. Amb_allergen.
IPR012334. Pectin_lyas_fold.
[Graphical view]

Gene3D

G3DSA:2.160.20.10. Pectin_lyas_fold. 1 hit.

Pfam

PF00544. Pec_lyase_C. 1 hit.
[Graphical view]

SMART

SM00656. Amb_all. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

PEL_BACSU

Accession

Primary (citable) accession number: P39116

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	June 16, 2009
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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