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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: 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)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

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

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-19211.

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)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...)2 Publications1

Keywords - PTMi

Glycoprotein

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
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi33 – 35Combined sources3
Beta strandi37 – 42Combined sources6
Beta strandi46 – 48Combined sources3
Beta strandi51 – 53Combined sources3
Helixi55 – 60Combined sources6
Helixi61 – 66Combined sources6
Helixi68 – 70Combined sources3
Helixi71 – 80Combined sources10
Turni86 – 88Combined sources3
Helixi95 – 99Combined sources5
Helixi104 – 118Combined sources15
Helixi121 – 137Combined sources17
Turni144 – 146Combined sources3
Helixi147 – 163Combined sources17
Helixi165 – 167Combined sources3
Helixi170 – 184Combined sources15
Beta strandi191 – 193Combined sources3
Beta strandi198 – 201Combined sources4
Helixi202 – 204Combined sources3
Helixi206 – 209Combined sources4
Helixi211 – 218Combined sources8
Turni219 – 222Combined sources4
Helixi225 – 236Combined sources12
Helixi238 – 245Combined sources8
Helixi246 – 248Combined sources3
Helixi254 – 275Combined sources22
Helixi283 – 289Combined sources7
Helixi290 – 294Combined sources5
Beta strandi312 – 314Combined sources3
Helixi319 – 329Combined sources11
Helixi332 – 339Combined sources8
Helixi346 – 348Combined sources3
Helixi349 – 355Combined sources7
Helixi365 – 367Combined sources3
Beta strandi370 – 374Combined sources5
Turni375 – 378Combined sources4
Beta strandi380 – 385Combined sources6
Beta strandi392 – 397Combined sources6
Beta strandi414 – 423Combined sources10
Beta strandi429 – 431Combined sources3
Helixi439 – 443Combined sources5
Turni444 – 446Combined sources3
Helixi448 – 450Combined sources3
Beta strandi451 – 457Combined sources7
Beta strandi468 – 472Combined sources5
Turni487 – 489Combined sources3
Helixi496 – 500Combined sources5
Turni501 – 503Combined sources3
Beta strandi508 – 516Combined sources9
Beta strandi518 – 520Combined sources3
Beta strandi522 – 529Combined sources8
Helixi531 – 533Combined sources3
Beta strandi538 – 549Combined sources12
Beta strandi553 – 555Combined sources3
Beta strandi557 – 569Combined sources13
Beta strandi572 – 582Combined sources11
Beta strandi585 – 587Combined sources3
Beta strandi590 – 594Combined sources5
Beta strandi602 – 611Combined sources10
Helixi613 – 615Combined sources3
Beta strandi616 – 623Combined sources8
Turni624 – 628Combined sources5
Beta strandi651 – 660Combined sources10
Beta strandi663 – 675Combined sources13
Beta strandi685 – 688Combined sources4
Beta strandi690 – 697Combined sources8
Beta strandi700 – 705Combined sources6
Beta strandi715 – 719Combined sources5
Beta strandi721 – 723Combined sources3
Beta strandi725 – 729Combined sources5
Beta strandi734 – 741Combined sources8
Beta strandi744 – 752Combined sources9
Turni754 – 756Combined sources3
Beta strandi759 – 763Combined sources5
Beta strandi765 – 771Combined sources7

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...

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

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)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.
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
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.

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

BioCyciMetaCyc:MONOMER-19211.

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: November 2, 2016
This is version 33 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.