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Protein

Heparin and heparin-sulfate lyase

Gene

hepB

Organism
Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.1 Publication

Catalytic activityi

Elimination of sulfate; appears to act on linkages between N-acetyl-D-glucosamine and uronate. Product is an unsaturated sugar.1 Publication
Eliminative cleavage of polysaccharides containing (1->4)-linked D-glucuronate or L-iduronate residues and (1->4)-alpha-linked 2-sulfoamino-2-deoxy-6-sulfo-D-glucose residues to give oligosaccharides with terminal 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei96N-acetyl-D-glucosamine1 Publication1
Binding sitei145N-acetyl-D-glucosamine1 Publication1
Binding sitei148N-acetyl-D-glucosamine1 Publication1
Binding sitei196N-acetyl-D-glucosamine1 Publication1
Active sitei2021 Publication1
Binding sitei205N-acetyl-D-glucosamine1 Publication1
Active sitei2571 Publication1
Binding sitei261N-acetyl-D-glucosamine1 Publication1
Binding sitei307N-acetyl-D-glucosamine1 Publication1
Binding sitei405N-acetyl-D-glucosamine1 Publication1
Active sitei4061 Publication1
Metal bindingi408Zinc; via pros nitrogen2 Publications1
Metal bindingi425Zinc2 Publications1
Binding sitei429N-acetyl-D-glucosamine1 Publication1
Metal bindingi451Zinc; via tele nitrogen2 Publications1
Binding sitei470N-acetyl-D-glucosamine; via amide nitrogen1 Publication1

GO - Molecular functioni

  • heparin binding Source: UniProtKB
  • heparin lyase activity Source: UniProtKB
  • heparin-sulfate lyase activity Source: UniProtKB-EC
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionLyase
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-19211
PHEP485917:G1GFH-2401-MONOMER

Protein family/group databases

CAZyiPL21 Polysaccharide Lyase Family 21

Names & Taxonomyi

Protein namesi
Recommended name:
Heparin and heparin-sulfate lyase
Alternative name(s):
Heparin lyase (EC:4.2.2.7)
Heparin-sulfate lyase (EC:4.2.2.8)
Heparinase II
Short name:
HepII
Gene namesi
Name:hepB
Ordered Locus Names:Phep_2408
OrganismiPedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)
Taxonomic identifieri485917 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesSphingobacteriiaSphingobacterialesSphingobacteriaceaePedobacter
Proteomesi
  • UP000000852 Componenti: Chromosome

Subcellular locationi

  • Periplasm 1 Publication

GO - Cellular componenti

  • periplasmic space Source: UniProtKB

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi202H → A: Loss of catalytic activity. 1 Publication1
Mutagenesisi257Y → F: Loss of catalytic activity. 1 Publication1
Mutagenesisi406H → A: Loss of catalytic activity. 1 Publication1
Mutagenesisi429Y → A or F: Impaired catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 251 PublicationAdd BLAST25
ChainiPRO_500014461326 – 772Heparin and heparin-sulfate lyaseAdd BLAST747

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi134O-linked (Man...) threonine2 Publications1

Keywords - PTMi

Glycoprotein

PTM databases

iPTMnetiC6XZB6

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi485917.Phep_2408

Structurei

Secondary structure

1772
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SMRiC6XZB6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni436 – 437N-acetyl-D-glucosamine binding2

Sequence similaritiesi

Belongs to the polysaccharide lyase 12 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4108PWI Bacteria
ENOG41100DU LUCA
KOiK19051
OMAiVYDWCYD
OrthoDBiPOG091H072P

Family and domain databases

Gene3Di1.50.10.100, 1 hit
InterProiView protein in InterPro
IPR008929 Chondroitin_lyas
IPR012480 Hepar_II_III
IPR032518 HepII_N
PfamiView protein in Pfam
PF16332 DUF4962, 1 hit
PF07940 Hepar_II_III, 1 hit
SUPFAMiSSF48230 SSF48230, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

C6XZB6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKRQLYLYVI FVVVELMVFT TKGYSQTKAD VVWKDVDGVS MPIPPKTHPR
60 70 80 90 100
LYLREQQVPD LKNRMNDPKL KKVWADMIKM QEDWKPADIP EVKDFRFYFN
110 120 130 140 150
QKGLTVRVEL MALNYLMTKD PKVGREAITS IIDTLETATF KPAGDISRGI
160 170 180 190 200
GLFMVTGAIV YDWCYDQLKP EEKTRFVKAF VRLAKMLECG YPPVKDKSIV
210 220 230 240 250
GHASEWMIMR DLLSVGIAIY DEFPEMYNLA AGRFFKEHLV ARNWFYPSHN
260 270 280 290 300
YHQGMSYLNV RFTNDLFALW ILDRMGAGNV FNPGQQFILY DAIYKRRPDG
310 320 330 340 350
QILAGGDVDY SRKKPKYYTM PALLAGSYYK DEYLNYEFLK DPNVEPHCKL
360 370 380 390 400
FEFLWRDTQL GSRKPDDLPL SRYSGSPFGW MIARTGWGPE SVIAEMKVNE
410 420 430 440 450
YSFLNHQHQD AGAFQIYYKG PLAIDAGSYT GSSGGYNSPH NKNFFKRTIA
460 470 480 490 500
HNSLLIYDPK ETFSSSGYGG SDHTDFAAND GGQRLPGKGW IAPRDLKEML
510 520 530 540 550
AGDFRTGKIL AQGFGPDNQT PDYTYLKGDI TAAYSAKVKE VKRSFLFLNL
560 570 580 590 600
KDAKVPAAMI VFDKVVASNP DFKKFWLLHS IEQPEIKGNQ ITIKRTKNGD
610 620 630 640 650
SGMLVNTALL PDAANSNITS IGGKGKDFWV FGTNYTNDPK PGTDEALERG
660 670 680 690 700
EWRVEITPKK AAAEDYYLNV IQIADNTQQK LHEVKRIDGD KVVGVQLADR
710 720 730 740 750
IVTFSKTSET VDRPFGFSVV GKGTFKFVMT DLLPGTWQVL KDGKILYPAL
760 770
SAKGDDGALY FEGTEGTYRF LR
Length:772
Mass (Da):87,626
Last modified:September 22, 2009 - v1
Checksum:i66D9752035421B99
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti505R → V AA sequence (PubMed:8702264).Curated1
Sequence conflicti758A → P in AAB18277 (PubMed:8702264).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U27585 Genomic DNA Translation: AAB18277.1
CP001681 Genomic DNA Translation: ACU04612.1
RefSeqiWP_015808224.1, NZ_AQGK01000001.1

Genome annotation databases

EnsemblBacteriaiACU04612; ACU04612; Phep_2408
KEGGiphe:Phep_2408

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U27585 Genomic DNA Translation: AAB18277.1
CP001681 Genomic DNA Translation: ACU04612.1
RefSeqiWP_015808224.1, NZ_AQGK01000001.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FUQX-ray2.15A/B27-772[»]
2FUTX-ray2.30A/B25-772[»]
3E7JX-ray2.10A/B24-772[»]
3E80X-ray2.35A/B/C27-772[»]
SMRiC6XZB6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi485917.Phep_2408

Protein family/group databases

CAZyiPL21 Polysaccharide Lyase Family 21

PTM databases

iPTMnetiC6XZB6

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACU04612; ACU04612; Phep_2408
KEGGiphe:Phep_2408

Phylogenomic databases

eggNOGiENOG4108PWI Bacteria
ENOG41100DU LUCA
KOiK19051
OMAiVYDWCYD
OrthoDBiPOG091H072P

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-19211
PHEP485917:G1GFH-2401-MONOMER

Family and domain databases

Gene3Di1.50.10.100, 1 hit
InterProiView protein in InterPro
IPR008929 Chondroitin_lyas
IPR012480 Hepar_II_III
IPR032518 HepII_N
PfamiView protein in Pfam
PF16332 DUF4962, 1 hit
PF07940 Hepar_II_III, 1 hit
SUPFAMiSSF48230 SSF48230, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiHEPB_PEDHD
AccessioniPrimary (citable) accession number: C6XZB6
Secondary accession number(s): Q46080
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 16, 2013
Last sequence update: September 22, 2009
Last modified: February 28, 2018
This is version 39 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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