EGCSE_RHOH1
ID EGCSE_RHOH1 Reviewed; 492 AA.
AC A0A3S5YBC7;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 10-APR-2019, sequence version 1.
DT 03-AUG-2022, entry version 16.
DE RecName: Full=Endoglycoceramidase I {ECO:0000303|PubMed:28179425};
DE Short=EGCase I {ECO:0000303|PubMed:28179425};
DE EC=3.2.1.123 {ECO:0000269|PubMed:28179425};
DE Flags: Precursor;
GN OrderedLocusNames=REQ_38260 {ECO:0000312|EMBL:CBH49814.1};
OS Rhodococcus hoagii (strain 103S) (Rhodococcus equi).
OC Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus.
OX NCBI_TaxID=685727 {ECO:0000312|Proteomes:UP000006892};
RN [1] {ECO:0000312|Proteomes:UP000006892}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=103S {ECO:0000312|Proteomes:UP000006892};
RX PubMed=20941392; DOI=10.1371/journal.pgen.1001145;
RA Letek M., Gonzalez P., Macarthur I., Rodriguez H., Freeman T.C.,
RA Valero-Rello A., Blanco M., Buckley T., Cherevach I., Fahey R., Hapeshi A.,
RA Holdstock J., Leadon D., Navas J., Ocampo A., Quail M.A., Sanders M.,
RA Scortti M.M., Prescott J.F., Fogarty U., Meijer W.G., Parkhill J.,
RA Bentley S.D., Vazquez-Boland J.A.;
RT "The genome of a pathogenic rhodococcus: cooptive virulence underpinned by
RT key gene acquisitions.";
RL PLoS Genet. 6:E1001145-E1001145(2010).
RN [2] {ECO:0007744|PDB:5CCU, ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z}
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 27-492 OF MUTANT SER-339 IN
RP COMPLEX WITH MONOSIALODIHEXOSYLGANGLIOSIDE (GM3) AND
RP MONOSIALOTETRAHEXOSYLGANGLIOSIDE (GM1), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, ACTIVE SITE, DISULFIDE
RP BONDS, AND MUTAGENESIS OF LYS-61; ASP-62; HIS-131; ASP-133; ASN-213;
RP ASN-265; GLN-298; TYR-302; GLU-339; ASP-342 AND TRP-365.
RX PubMed=28179425; DOI=10.1074/jbc.m116.763821;
RA Han Y.B., Chen L.Q., Li Z., Tan Y.M., Feng Y., Yang G.Y.;
RT "Structural Insights into the Broad Substrate Specificity of a Novel
RT Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases.";
RL J. Biol. Chem. 292:4789-4800(2017).
CC -!- FUNCTION: Hydrolyzes glycosphingolipids; exhibits broad substrate
CC specificity including monosialodihexosylganglioside (GM3),
CC monosialotetrahexosylganglioside (GM1), fucosyl-GM1, lactosylceramide,
CC globotriosylceramide, globotetraosylceramide, ganglioside GD1a, and
CC ganglioside GD1b (PubMed:28179425). No activity towards
CC glucosylceramide and galactosylceramide (PubMed:28179425).
CC {ECO:0000269|PubMed:28179425}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an oligoglycosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide + H2O
CC = an N-acyl-sphingoid base + an oligoglycosyl-(1->4)-D-glucose;
CC Xref=Rhea:RHEA:22288, ChEBI:CHEBI:15377, ChEBI:CHEBI:83273,
CC ChEBI:CHEBI:136875, ChEBI:CHEBI:156536; EC=3.2.1.123;
CC Evidence={ECO:0000269|PubMed:28179425};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:22289;
CC Evidence={ECO:0000269|PubMed:28179425};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ganglioside GM3 + H2O = an N-acyl-sphingoid base + N-acetyl-
CC alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-D-glucose;
CC Xref=Rhea:RHEA:65540, ChEBI:CHEBI:15377, ChEBI:CHEBI:79210,
CC ChEBI:CHEBI:83273, ChEBI:CHEBI:156068;
CC Evidence={ECO:0000269|PubMed:28179425};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:65541;
CC Evidence={ECO:0000269|PubMed:28179425};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ganglioside GM1 + H2O = an N-acyl-sphingoid base + beta-D-Gal-
CC (1->3)-beta-D-GalNAc-(1->4)-[alpha-Neu5Ac-(2->3)]-beta-D-Gal-(1->4)-
CC D-Glc; Xref=Rhea:RHEA:65544, ChEBI:CHEBI:15377, ChEBI:CHEBI:82639,
CC ChEBI:CHEBI:83273, ChEBI:CHEBI:156537;
CC Evidence={ECO:0000269|PubMed:28179425};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:65545;
CC Evidence={ECO:0000269|PubMed:28179425};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ganglioside Fuc-GM1 + H2O = alpha-Fuc-(1->2)-beta-Gal-(1->3)-
CC beta-GalNAc-(1->4)-[alpha-Neu5Ac-(2->3)]-beta-Gal-(1->4)-Glc + an N-
CC acyl-sphingoid base; Xref=Rhea:RHEA:65548, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:83273, ChEBI:CHEBI:90189, ChEBI:CHEBI:156538;
CC Evidence={ECO:0000269|PubMed:28179425};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:65549;
CC Evidence={ECO:0000269|PubMed:28179425};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide +
CC H2O = an N-acyl-sphingoid base + lactose; Xref=Rhea:RHEA:65552,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17716, ChEBI:CHEBI:79208,
CC ChEBI:CHEBI:83273; Evidence={ECO:0000269|PubMed:28179425};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:65553;
CC Evidence={ECO:0000269|PubMed:28179425};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.23 mM for monosialotetrahexosylganglioside (GM1)
CC {ECO:0000269|PubMed:28179425};
CC Note=kcat is 10.5 sec(-1) with monosialotetrahexosylganglioside as
CC substrate. {ECO:0000269|PubMed:28179425};
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:28179425}. Membrane
CC {ECO:0000255|PROSITE-ProRule:PRU00303}; Lipid-anchor
CC {ECO:0000255|PROSITE-ProRule:PRU00303}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 5 (cellulase A) family.
CC {ECO:0000305}.
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DR EMBL; FN563149; CBH49814.1; -; Genomic_DNA.
DR RefSeq; WP_013417039.1; NC_014659.1.
DR PDB; 5CCU; X-ray; 2.11 A; A/B=27-492.
DR PDB; 5J14; X-ray; 1.92 A; A/B=27-492.
DR PDB; 5J7Z; X-ray; 2.15 A; A/B=27-492.
DR PDBsum; 5CCU; -.
DR PDBsum; 5J14; -.
DR PDBsum; 5J7Z; -.
DR AlphaFoldDB; A0A3S5YBC7; -.
DR SMR; A0A3S5YBC7; -.
DR STRING; 685727.REQ_38260; -.
DR EnsemblBacteria; CBH49814; CBH49814; REQ_38260.
DR KEGG; req:REQ_38260; -.
DR BRENDA; 3.2.1.123; 1646.
DR Proteomes; UP000006892; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0047876; F:endoglycosylceramidase activity; IDA:UniProtKB.
DR GO; GO:0006683; P:galactosylceramide catabolic process; IDA:UniProtKB.
DR Gene3D; 2.60.40.1180; -; 1.
DR InterPro; IPR041036; GH5_C.
DR InterPro; IPR001547; Glyco_hydro_5.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR Pfam; PF00150; Cellulase; 1.
DR Pfam; PF18564; Glyco_hydro_5_C; 1.
DR SUPFAM; SSF51445; SSF51445; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Glycosidase; Hydrolase; Lipid metabolism;
KW Lipoprotein; Membrane; Palmitate; Secreted; Signal;
KW Sphingolipid metabolism.
FT SIGNAL 1..14
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT CHAIN 15..492
FT /note="Endoglycoceramidase I"
FT /evidence="ECO:0000255"
FT /id="PRO_5018576037"
FT REGION 467..492
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 214
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:O85465"
FT ACT_SITE 339
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:28179425"
FT BINDING 61
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 62
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J7Z"
FT BINDING 131..133
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 213..214
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 265
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 298
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 302
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT BINDING 365
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5J14, ECO:0007744|PDB:5J7Z"
FT LIPID 15
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT LIPID 15
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT DISULFID 224..229
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5CCU, ECO:0007744|PDB:5J14,
FT ECO:0007744|PDB:5J7Z"
FT DISULFID 294..313
FT /evidence="ECO:0000269|PubMed:28179425,
FT ECO:0007744|PDB:5CCU, ECO:0007744|PDB:5J14,
FT ECO:0007744|PDB:5J7Z"
FT MUTAGEN 61
FT /note="K->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 62
FT /note="D->A: Decreases enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 131
FT /note="H->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 133
FT /note="D->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 213
FT /note="N->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 265
FT /note="N->A: Severely decreases enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 298
FT /note="Q->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 302
FT /note="Y->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 339
FT /note="E->S: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 342
FT /note="D->A,E,F,K,L,W,Y: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 342
FT /note="D->N,Q: Severely decreases enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT MUTAGEN 365
FT /note="W->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:28179425"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 62..64
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 74..82
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 94..97
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 106..121
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 125..130
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 133..136
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:5J14"
FT TURN 180..183
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 185..200
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 206..210
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 221..224
FT /evidence="ECO:0007829|PDB:5J14"
FT TURN 225..227
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 230..250
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 262..266
FT /evidence="ECO:0007829|PDB:5J14"
FT TURN 275..277
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 283..288
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 295..303
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 307..312
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 313..331
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 335..337
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:5J14"
FT TURN 345..347
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 348..358
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 361..365
FT /evidence="ECO:0007829|PDB:5J14"
FT HELIX 379..384
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 388..401
FT /evidence="ECO:0007829|PDB:5J14"
FT TURN 403..405
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 408..414
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 421..424
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 427..429
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 435..443
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 450..460
FT /evidence="ECO:0007829|PDB:5J14"
FT STRAND 462..467
FT /evidence="ECO:0007829|PDB:5J14"
SQ SEQUENCE 492 AA; 52830 MW; 3F24E87C8B43BE2F CRC64;
MRKTVVAFAA AIAACSAVLS STTTSAAPPA TPITTLQADG THLVDGYGRT VLLHGVNNVD
KDAPYLPAGE TLTPQDIDIL VRHGFNTVRL GTSFDALMPQ RGQIDEAYLD RLTGVVDALT
ARGMHVLLDN HQDGLSKAWG GNGFPEWAIE SRPREWEPNP GFPLYYLMPS LNAGWDEVWG
NTHGALDHLG TALGALAERV EGKPGVMGIE LLNEPWPGSR FLSCFPNGCP DFDRTYQAAM
QKLTDAVRAQ NPTIPVYWEP NVTWNQMMPS NLFAPPVTPA LTTADVVFAP HDYCIPSQLA
IYLGLPQALR GLCVPQQDLT WSNIDAITER ANVPTVITEF GDGDPTVLKN TLARADERFI
GWQYWHFGAG NATDPFLGEV GRQLVRTYPQ ATAGEPGRMI FDADNGDFAY RFTPRAATRP
TEIFVSDLHY PDGYAVQVDG GQVTSAPGAR IVTVVADGSG PVTVKINRPG SAGAEVPDGP
IETSSSGSSG SS
