HEPC_PEDHD
ID HEPC_PEDHD Reviewed; 659 AA.
AC Q59289; C6XUY0;
DT 16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Heparin-sulfate lyase;
DE EC=4.2.2.8;
DE AltName: Full=Heparin-sulfate eliminase;
DE AltName: Full=Heparinase III;
DE Short=HepIII;
DE AltName: Full=Heparitin-sulfate lyase;
DE Flags: Precursor;
GN Name=hepC; OrderedLocusNames=Phep_3797;
OS Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457
OS / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3).
OC Bacteria; Bacteroidetes; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Pedobacter.
OX NCBI_TaxID=485917;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS, PROTEIN
RP SEQUENCE OF 99-123; 128-142 AND 414-436, FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB
RC 9290 / NRRL B-14731 / HIM 762-3;
RX PubMed=8702264; DOI=10.1128/aem.62.8.2723-2734.1996;
RA Su H., Blain F., Musil R.A., Zimmermann J.J., Gu K., Bennett D.C.;
RT "Isolation and expression in Escherichia coli of hepB and hepC, genes
RT coding for the glycosaminoglycan-degrading enzymes heparinase II and
RT heparinase III, respectively, from Flavobacterium heparinum.";
RL Appl. Environ. Microbiol. 62:2723-2734(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 62-68; 75-88;
RP 249-264; 383-390; 404-408; 459-464; 468-483; 513-519; 597-605 AND 625-631.
RX PubMed=8780685; DOI=10.1006/bbrc.1996.1246;
RA Godavarti R., Davis M., Venkataraman G., Cooney C., Langer R.,
RA Sasisekharan R.;
RT "Heparinase III from Flavobacterium heparinum: cloning and recombinant
RT expression in Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 225:751-758(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB
RC 9290 / NRRL B-14731 / HIM 762-3;
RX PubMed=21304637; DOI=10.4056/sigs.22138;
RA Han C., Spring S., Lapidus A., Del Rio T.G., Tice H., Copeland A.,
RA Cheng J.F., Lucas S., Chen F., Nolan M., Bruce D., Goodwin L., Pitluck S.,
RA Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K.,
RA Land M., Hauser L., Chang Y.J., Jeffries C.C., Saunders E., Chertkov O.,
RA Brettin T., Goker M., Rohde M., Bristow J., Eisen J.A., Markowitz V.,
RA Hugenholtz P., Kyrpides N.C., Klenk H.P., Detter J.C.;
RT "Complete genome sequence of Pedobacter heparinus type strain (HIM 762-
RT 3).";
RL Stand. Genomic Sci. 1:54-62(2009).
RN [4]
RP IDENTIFICATION.
RX PubMed=2211596; DOI=10.1016/s0021-9258(17)44833-2;
RA Nader H.B., Porcionatto M.A., Tersariol I.L., Pinhal M.A., Oliveira F.W.,
RA Moraes C.T., Dietrich C.P.;
RT "Purification and substrate specificity of heparitinase I and heparitinase
RT II from Flavobacterium heparinum. Analyses of the heparin and heparan
RT sulfate degradation products by 13C NMR spectroscopy.";
RL J. Biol. Chem. 265:16807-16813(1990).
RN [5]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF HIS-295 AND
RP HIS-510.
RX PubMed=10747789; DOI=10.1021/bi992514k;
RA Pojasek K., Shriver Z., Hu Y., Sasisekharan R.;
RT "Histidine 295 and histidine 510 are crucial for the enzymatic degradation
RT of heparan sulfate by heparinase III.";
RL Biochemistry 39:4012-4019(2000).
CC -!- FUNCTION: Specifically cleaves heparan sulfate-rich regions of acidic
CC polysaccharides. Does not act on N,O-desulfated glucosamine or N-
CC acetyl-O-sulfated glucosamine linkages. Functions in cleaving metazoan
CC heparan sulfate and providing carbon, nitrogen and sulfate sources for
CC microorganisms. {ECO:0000269|PubMed:10747789,
CC ECO:0000269|PubMed:8702264}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Elimination of sulfate, appears to act on linkages between N-
CC acetyl-D-glucosamine and uronate. Product is an unsaturated sugar.;
CC EC=4.2.2.8; Evidence={ECO:0000269|PubMed:8702264};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=143 uM for heparan sulfate {ECO:0000269|PubMed:10747789};
CC KM=80 uM for heparan sulfate (with recombinant enzyme)
CC {ECO:0000269|PubMed:10747789};
CC Note=kcat is 94 sec(-1). kcat is 78 sec(-1) with recombinant enzyme.;
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:8702264}.
CC -!- SIMILARITY: Belongs to the polysaccharide lyase 12 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ACU05988.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U27586; AAB18278.1; -; Genomic_DNA.
DR EMBL; CP001681; ACU05988.1; ALT_INIT; Genomic_DNA.
DR PIR; JC4910; JC4910.
DR RefSeq; WP_036674924.1; NZ_AQGK01000003.1.
DR PDB; 4MMH; X-ray; 2.20 A; A=25-659.
DR PDB; 4MMI; X-ray; 2.40 A; A=25-659.
DR PDBsum; 4MMH; -.
DR PDBsum; 4MMI; -.
DR AlphaFoldDB; Q59289; -.
DR SMR; Q59289; -.
DR STRING; 485917.Phep_3797; -.
DR CAZy; PL12; Polysaccharide Lyase Family 12.
DR PRIDE; Q59289; -.
DR EnsemblBacteria; ACU05988; ACU05988; Phep_3797.
DR KEGG; phe:Phep_3797; -.
DR eggNOG; COG5434; Bacteria.
DR HOGENOM; CLU_013047_1_0_10; -.
DR BioCyc; MetaCyc:MON-19212; -.
DR BRENDA; 4.2.2.8; 2286.
DR Proteomes; UP000000852; Chromosome.
DR GO; GO:0042597; C:periplasmic space; TAS:UniProtKB.
DR GO; GO:0015021; F:heparin-sulfate lyase activity; IDA:UniProtKB.
DR GO; GO:0030200; P:heparan sulfate proteoglycan catabolic process; IDA:UniProtKB.
DR Gene3D; 1.50.10.100; -; 1.
DR InterPro; IPR008929; Chondroitin_lyas.
DR InterPro; IPR012480; Hepar_II_III.
DR InterPro; IPR031680; Hepar_II_III_N.
DR Pfam; PF07940; Hepar_II_III; 1.
DR Pfam; PF16889; Hepar_II_III_N; 1.
DR SUPFAM; SSF48230; SSF48230; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Periplasm;
KW Reference proteome; Signal.
FT SIGNAL 1..24
FT /evidence="ECO:0000269|PubMed:8702264"
FT CHAIN 25..659
FT /note="Heparin-sulfate lyase"
FT /id="PRO_5000144614"
FT ACT_SITE 294
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT MUTAGEN 295
FT /note="H->A: Impaired catalytic activity."
FT /evidence="ECO:0000269|PubMed:10747789"
FT MUTAGEN 510
FT /note="H->A: Impaired catalytic activity."
FT /evidence="ECO:0000269|PubMed:10747789"
FT CONFLICT 128..129
FT /note="PV -> LI (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 45..52
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 56..72
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 93..103
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 119..122
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 132..138
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 143..154
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 157..173
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 180..186
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 189..206
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 214..232
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 242..255
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 262..280
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 292..310
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 311..313
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 320..335
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 354..367
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 372..378
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 379..381
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 390..394
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 395..398
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 399..404
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 411..416
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 432..436
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 439..442
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 454..463
FT /evidence="ECO:0007829|PDB:4MMH"
FT HELIX 466..468
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 469..474
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 485..490
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 493..505
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 508..517
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 518..520
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 521..531
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 534..541
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 549..551
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 552..555
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 556..558
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 564..571
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 578..582
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 585..589
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 592..595
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 598..605
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 607..609
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 611..624
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 628..632
FT /evidence="ECO:0007829|PDB:4MMH"
FT TURN 638..641
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 642..649
FT /evidence="ECO:0007829|PDB:4MMH"
FT STRAND 652..659
FT /evidence="ECO:0007829|PDB:4MMH"
SQ SEQUENCE 659 AA; 75807 MW; B73EDF10A1256FE2 CRC64;
MTTKIFKRII VFAVIALSSG NILAQSSSIT RKDFDHINLE YSGLEKVNKA VAAGNYDDAA
KALLAYYREK SKAREPDFSN AEKPADIRQP IDKVTREMAD KALVHQFQPH KGYGYFDYGK
DINWQMWPVK DNEVRWQLHR VKWWQAMALV YHATGDEKYA REWVYQYSDW ARKNPLGLSQ
DNDKFVWRPL EVSDRVQSLP PTFSLFVNSP AFTPAFLMEF LNSYHQQADY LSTHYAEQGN
HRLFEAQRNL FAGVSFPEFK DSPRWRQTGI SVLNTEIKKQ VYADGMQFEL SPIYHVAAID
IFLKAYGSAK RVNLEKEFPQ SYVQTVENMI MALISISLPD YNTPMFGDSW ITDKNFRMAQ
FASWARVFPA NQAIKYFATD GKQGKAPNFL SKALSNAGFY TFRSGWDKNA TVMVLKASPP
GEFHAQPDNG TFELFIKGRN FTPDAGVFVY SGDEAIMKLR NWYRQTRIHS TLTLDNQNMV
ITKARQNKWE TGNNLDVLTY TNPSYPNLDH QRSVLFINKK YFLVIDRAIG EATGNLGVHW
QLKEDSNPVF DKTKNRVYTT YRDGNNLMIQ SLNADRTSLN EEEGKVSYVY NKELKRPAFV
FEKPKKNAGT QNFVSIVYPY DGQKAPEISI RENKGNDFEK GKLNLTLTIN GKQQLVLVP
