Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei96 – 961N-acetyl-D-glucosamine1 Publication
Binding sitei145 – 1451N-acetyl-D-glucosamine1 Publication
Binding sitei148 – 1481N-acetyl-D-glucosamine1 Publication
Binding sitei196 – 1961N-acetyl-D-glucosamine1 Publication
Active sitei202 – 20211 Publication
Binding sitei205 – 2051N-acetyl-D-glucosamine1 Publication
Active sitei257 – 25711 Publication
Binding sitei261 – 2611N-acetyl-D-glucosamine1 Publication
Binding sitei307 – 3071N-acetyl-D-glucosamine1 Publication
Binding sitei405 – 4051N-acetyl-D-glucosamine1 Publication
Active sitei406 – 40611 Publication
Metal bindingi408 – 4081Zinc; via pros nitrogen2 Publications
Metal bindingi425 – 4251Zinc2 Publications
Binding sitei429 – 4291N-acetyl-D-glucosamine1 Publication
Metal bindingi451 – 4511Zinc; via tele nitrogen2 Publications
Binding sitei470 – 4701N-acetyl-D-glucosamine; via amide nitrogen1 Publication

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

  • heparin catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciPHEP485917:GHL9-2432-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
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi202 – 2021H → A: Loss of catalytic activity. 1 Publication
Mutagenesisi257 – 2571Y → F: Loss of catalytic activity. 1 Publication
Mutagenesisi406 – 4061H → A: Loss of catalytic activity. 1 Publication
Mutagenesisi429 – 4291Y → A or F: Impaired catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 25251 PublicationAdd
BLAST
Chaini26 – 772747Heparin and heparin-sulfate lyasePRO_5000144613Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi134 – 1341O-linked (Man...)2 Publications

Keywords - PTMi

Glycoprotein

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi485917.Phep_2408.

Structurei

Secondary structure

1
772
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi33 – 353Combined sources
Beta strandi37 – 426Combined sources
Beta strandi46 – 483Combined sources
Beta strandi51 – 533Combined sources
Helixi55 – 606Combined sources
Helixi61 – 666Combined sources
Helixi68 – 703Combined sources
Helixi71 – 8010Combined sources
Turni86 – 883Combined sources
Helixi95 – 995Combined sources
Helixi104 – 11815Combined sources
Helixi121 – 13717Combined sources
Turni144 – 1463Combined sources
Helixi147 – 16317Combined sources
Helixi165 – 1673Combined sources
Helixi170 – 18415Combined sources
Beta strandi191 – 1933Combined sources
Beta strandi198 – 2014Combined sources
Helixi202 – 2043Combined sources
Helixi206 – 2094Combined sources
Helixi211 – 2188Combined sources
Turni219 – 2224Combined sources
Helixi225 – 23612Combined sources
Helixi238 – 2458Combined sources
Helixi246 – 2483Combined sources
Helixi254 – 27522Combined sources
Helixi283 – 2897Combined sources
Helixi290 – 2945Combined sources
Beta strandi312 – 3143Combined sources
Helixi319 – 32911Combined sources
Helixi332 – 3398Combined sources
Helixi346 – 3483Combined sources
Helixi349 – 3557Combined sources
Helixi365 – 3673Combined sources
Beta strandi370 – 3745Combined sources
Turni375 – 3784Combined sources
Beta strandi380 – 3856Combined sources
Beta strandi392 – 3976Combined sources
Beta strandi414 – 42310Combined sources
Beta strandi429 – 4313Combined sources
Helixi439 – 4435Combined sources
Turni444 – 4463Combined sources
Helixi448 – 4503Combined sources
Beta strandi451 – 4577Combined sources
Beta strandi468 – 4725Combined sources
Turni487 – 4893Combined sources
Helixi496 – 5005Combined sources
Turni501 – 5033Combined sources
Beta strandi508 – 5169Combined sources
Beta strandi518 – 5203Combined sources
Beta strandi522 – 5298Combined sources
Helixi531 – 5333Combined sources
Beta strandi538 – 54912Combined sources
Beta strandi553 – 5553Combined sources
Beta strandi557 – 56913Combined sources
Beta strandi572 – 58211Combined sources
Beta strandi585 – 5873Combined sources
Beta strandi590 – 5945Combined sources
Beta strandi602 – 61110Combined sources
Helixi613 – 6153Combined sources
Beta strandi616 – 6238Combined sources
Turni624 – 6285Combined sources
Beta strandi651 – 66010Combined sources
Beta strandi663 – 67513Combined sources
Beta strandi685 – 6884Combined sources
Beta strandi690 – 6978Combined sources
Beta strandi700 – 7056Combined sources
Beta strandi715 – 7195Combined sources
Beta strandi721 – 7233Combined sources
Beta strandi725 – 7295Combined sources
Beta strandi734 – 7418Combined sources
Beta strandi744 – 7529Combined sources
Turni754 – 7563Combined sources
Beta strandi759 – 7635Combined sources
Beta strandi765 – 7717Combined sources

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni436 – 4372N-acetyl-D-glucosamine binding

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

InterProiIPR008929. Chondroitin_lyas.
IPR012480. Hepar_II_III.
[Graphical view]
PfamiPF07940. Hepar_II_III. 1 hit.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti505 – 5051R → V AA sequence (PubMed:8702264).Curated
Sequence conflicti758 – 7581A → P in AAB18277 (PubMed:8702264).Curated

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.
PATRICi22881893. VBIPedHep98714_2423.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2FUQX-ray2.15A/B27-772[»]
2FUTX-ray2.30A/B25-772[»]
3E7JX-ray2.10A/B24-772[»]
3E80X-ray2.35A/B/C27-772[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi485917.Phep_2408.

Protein family/group databases

CAZyiPL21. Polysaccharide Lyase Family 21.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACU04612; ACU04612; Phep_2408.
KEGGiphe:Phep_2408.
PATRICi22881893. VBIPedHep98714_2423.

Phylogenomic databases

eggNOGiENOG4108PWI. Bacteria.
ENOG41100DU. LUCA.
KOiK19051.
OMAiVYDWCYD.
OrthoDBiPOG091H072P.

Enzyme and pathway databases

BioCyciPHEP485917:GHL9-2432-MONOMER.

Family and domain databases

InterProiIPR008929. Chondroitin_lyas.
IPR012480. Hepar_II_III.
[Graphical view]
PfamiPF07940. Hepar_II_III. 1 hit.
[Graphical view]
SUPFAMiSSF48230. SSF48230. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHEPB_PEDHD
AccessioniPrimary (citable) accession number: C6XZB6
Secondary accession number(s): Q46080
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 16, 2013
Last sequence update: September 22, 2009
Last modified: September 7, 2016
This is version 32 of the entry and version 1 of the sequence. [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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.