RHA78_STRAW
ID RHA78_STRAW Reviewed; 1030 AA.
AC Q82PP4;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Alpha-L-rhamnosidase {ECO:0000303|PubMed:23486481};
DE EC=3.2.1.40 {ECO:0000269|PubMed:23291751};
DE AltName: Full=Rha78A {ECO:0000303|PubMed:23486481};
GN ORFNames=SAVERM_828;
OS Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC
OS 14893 / NCIMB 12804 / NRRL 8165 / MA-4680).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=227882;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL
RC 8165 / MA-4680;
RX PubMed=11572948; DOI=10.1073/pnas.211433198;
RA Omura S., Ikeda H., Ishikawa J., Hanamoto A., Takahashi C., Shinose M.,
RA Takahashi Y., Horikawa H., Nakazawa H., Osonoe T., Kikuchi H., Shiba T.,
RA Sakaki Y., Hattori M.;
RT "Genome sequence of an industrial microorganism Streptomyces avermitilis:
RT deducing the ability of producing secondary metabolites.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:12215-12220(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL
RC 8165 / MA-4680;
RX PubMed=12692562; DOI=10.1038/nbt820;
RA Ikeda H., Ishikawa J., Hanamoto A., Shinose M., Kikuchi H., Shiba T.,
RA Sakaki Y., Hattori M., Omura S.;
RT "Complete genome sequence and comparative analysis of the industrial
RT microorganism Streptomyces avermitilis.";
RL Nat. Biotechnol. 21:526-531(2003).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBSTRATE
RP SPECIFICITY.
RX PubMed=23291751; DOI=10.1271/bbb.120735;
RA Ichinose H., Fujimoto Z., Kaneko S.;
RT "Characterization of an alpha-L-Rhamnosidase from Streptomyces
RT avermitilis.";
RL Biosci. Biotechnol. Biochem. 77:213-216(2013).
RN [4] {ECO:0007744|PDB:3W5M, ECO:0007744|PDB:3W5N}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CALCIUM AND
RP L-RHAMNOSE, AND MUTAGENESIS OF ASP-179; ASN-180; GLU-636 AND GLU-895.
RX PubMed=23486481; DOI=10.1074/jbc.m113.460097;
RA Fujimoto Z., Jackson A., Michikawa M., Maehara T., Momma M., Henrissat B.,
RA Gilbert H.J., Kaneko S.;
RT "The structure of a Streptomyces avermitilis alpha-L-rhamnosidase reveals a
RT novel carbohydrate-binding module CBM67 within the six-domain
RT arrangement.";
RL J. Biol. Chem. 288:12376-12385(2013).
CC -!- FUNCTION: Alpha-L-rhamnosidase which is able to degrade p-nitrophenyl-
CC alpha-L-rhamnopyranoside (PNP-Rha) in vitro. Releases L-rhamnose from
CC citrus flavonoids such as naringin, rutin and hesperidin, and the
CC arabinogalactan-protein (AGP) gum arabic. AGPs are a family of
CC proteoglycans that are localized on the cell surfaces of higher plants.
CC Cleaves both the alpha-1,6 and the alpha-1,2-linked rhamnosyl residues.
CC {ECO:0000269|PubMed:23291751}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of terminal non-reducing alpha-L-rhamnose residues
CC in alpha-L-rhamnosides.; EC=3.2.1.40;
CC Evidence={ECO:0000269|PubMed:23291751};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.03 mM for p-nitrophenyl-alpha-L-rhamnopyranoside
CC {ECO:0000269|PubMed:23291751};
CC Note=kcat is 1.93 sec(-1) with p-nitrophenyl-alpha-L-rhamnopyranoside
CC as substrate. {ECO:0000269|PubMed:23291751};
CC pH dependence:
CC Optimum pH is 6. {ECO:0000269|PubMed:23291751};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius.
CC {ECO:0000269|PubMed:23291751};
CC -!- DOMAIN: The carbohydrate-binding module-67 (CBM67) binds L-rhamnose, it
CC does not bind L-galactose or L-fucose, demonstrating that
CC stereochemistry of the sugar at C4 and/or C2 are important specificity
CC determinants. Also, removal of calcium through chelation or mutation
CC abrogates L-rhamnose binding, confirming the importance of calcium in
CC the binding of its ligand. {ECO:0000269|PubMed:23291751}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 78 family. {ECO:0000305}.
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DR EMBL; BA000030; BAC68538.1; -; Genomic_DNA.
DR PDB; 3W5M; X-ray; 1.80 A; A=1-1030.
DR PDB; 3W5N; X-ray; 1.80 A; A=1-1030.
DR PDBsum; 3W5M; -.
DR PDBsum; 3W5N; -.
DR AlphaFoldDB; Q82PP4; -.
DR SMR; Q82PP4; -.
DR STRING; 227882.SAV_828; -.
DR EnsemblBacteria; BAC68538; BAC68538; SAVERM_828.
DR KEGG; sma:SAVERM_828; -.
DR eggNOG; COG3250; Bacteria.
DR HOGENOM; CLU_002926_3_0_11; -.
DR OMA; HYHPPNT; -.
DR BioCyc; MetaCyc:MON-20550; -.
DR Proteomes; UP000000428; Chromosome.
DR GO; GO:0030596; F:alpha-L-rhamnosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR Gene3D; 1.50.10.10; -; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR008928; 6-hairpin_glycosidase_sf.
DR InterPro; IPR012341; 6hp_glycosidase-like_sf.
DR InterPro; IPR016007; Alpha_rhamnosid.
DR InterPro; IPR035396; Bac_rhamnosid6H.
DR InterPro; IPR035398; Bac_rhamnosid_C.
DR InterPro; IPR013737; Bac_rhamnosid_N.
DR InterPro; IPR036116; FN3_sf.
DR InterPro; IPR008979; Galactose-bd-like_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR008902; Rhamnosid_concanavalin.
DR Pfam; PF05592; Bac_rhamnosid; 1.
DR Pfam; PF17389; Bac_rhamnosid6H; 1.
DR Pfam; PF17390; Bac_rhamnosid_C; 1.
DR Pfam; PF08531; Bac_rhamnosid_N; 1.
DR PIRSF; PIRSF010631; A-rhamnsds; 1.
DR SUPFAM; SSF48208; SSF48208; 1.
DR SUPFAM; SSF49265; SSF49265; 1.
DR SUPFAM; SSF49785; SSF49785; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..1030
FT /note="Alpha-L-rhamnosidase"
FT /id="PRO_0000448313"
FT REGION 133..297
FT /note="Carbohydrate-binding module-67 (CBM67)"
FT /evidence="ECO:0000305|PubMed:23486481"
FT ACT_SITE 636
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:23486481"
FT ACT_SITE 895
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:23486481"
FT BINDING 179..180
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 179
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0007744|PDB:3W5M, ECO:0007744|PDB:3W5N"
FT BINDING 180
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0007744|PDB:3W5M"
FT BINDING 203
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 228
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 233
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0007744|PDB:3W5M, ECO:0007744|PDB:3W5N"
FT BINDING 630
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 634..636
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 643
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 695
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:3W5N"
FT BINDING 916
FT /ligand="alpha-L-rhamnose"
FT /ligand_id="ChEBI:CHEBI:27907"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:3W5N"
FT MUTAGEN 179
FT /note="D->A: Abrogates L-rhamnose binding."
FT /evidence="ECO:0000269|PubMed:23486481"
FT MUTAGEN 180
FT /note="N->A: Abrogates L-rhamnose binding."
FT /evidence="ECO:0000269|PubMed:23486481"
FT MUTAGEN 636
FT /note="E->D,Q: Drastically reduces alpha-L-rhamnosidase
FT activity."
FT /evidence="ECO:0000269|PubMed:23486481"
FT MUTAGEN 895
FT /note="E->D,Q: Drastically reduces alpha-L-rhamnosidase
FT activity."
FT /evidence="ECO:0000269|PubMed:23486481"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 40..51
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 85..97
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 127..130
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 144..147
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 148..150
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 156..165
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 171..186
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 217..227
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 229..232
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 235..244
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 247..254
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 257..262
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 266..269
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 282..286
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 303..311
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 316..333
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 350..352
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 353..360
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 362..364
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 367..377
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 379..382
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 398..407
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 412..416
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 427..432
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 433..435
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 436..440
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 441..443
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 446..449
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 458..460
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 470..474
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 480..487
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 490..495
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 498..515
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 522..531
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 540..542
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 548..552
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 557..561
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 568..577
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 584..586
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 587..595
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 600..605
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 607..622
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 624..628
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 632..635
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 641..654
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 658..671
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 679..683
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 693..697
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 698..710
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 713..732
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 756..777
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 783..800
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 812..820
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 826..828
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 829..842
FT /evidence="ECO:0007829|PDB:3W5M"
FT TURN 851..853
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 854..863
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 867..875
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 878..882
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 883..887
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 918..922
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 923..929
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 934..937
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 938..940
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 942..945
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 955..962
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 965..974
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 977..984
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 989..995
FT /evidence="ECO:0007829|PDB:3W5M"
FT HELIX 999..1001
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 1003..1013
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 1016..1021
FT /evidence="ECO:0007829|PDB:3W5M"
FT STRAND 1023..1030
FT /evidence="ECO:0007829|PDB:3W5M"
SQ SEQUENCE 1030 AA; 111886 MW; 7E9D6E2852C27764 CRC64;
MSALRVTSPS VEYVQRPLGL DAAHPRLSWP MASAAPGRRQ SAYQVRVASS AAGLSHPDVW
DSGKVVSDDS VLVPYAGPPL KPRTRYFWSV RVWDADGGAS EWSAPSWWET GLMGASQWSA
KWISAPAPLT EAPSLEGSSW IWFPEGEPAN SAPAATRWFR RTVDLPDDIT GATLAISADN
VYAVSVDGAE VARTDLEADN EGWRRPAVID VLDHVHSGNN TLAVSASNAS VGPAGWICVL
VLTTASGEKK IFSDASWKST DHEPADGWRE PDFDDSGWPA AKVAAAWGAG PWGRVAPVAS
AANQLRHEFR LPHKKVSRAR LYATALGLYE AHLNGRRVGR DQLAPGWTDY RKRVQYQTYD
VTSSVRPGAN ALAAYVAPGW YAGNVGMFGP HQYGERPALL AQLEVEYADG TSERITSGPD
WRAASGPIVS ADLLSGETYD ARKETAGWTS PGFDDRAWLA VRGADNDVPE QIVAQVDGPV
RIAKELPARK VTEPKPGVFV LDLGQNMVGS VRLRVSGDAG TTVRLRHAEV LNPDGTIYTA
NLRSAAATDT YTLKGQGEET YEPRFTFHGF RYVEVTGFPG KPSTTSVTGR VMHTSAPFTF
EFETNVPMLN KLHSNITWGQ RGNFLSVPTD TPARDERLGW TGDINVFAPT AAYTMESARF
LTKWLVDLRD AQTSDGAFTD VAPAVGNLGN GVAGWGDAGV TVPWALYQAY GDRQVLADAL
PSVHAWLRYL EKHSDGLLRP ADGYGDWLNV SDETPKDVIA TAYFAHSADL AARMATELGK
DAAPYTDLFT RIRKAFQTAY VASDGKVKGD TQSAYVLTLS MNLVPDALRK AAADRLVALI
EAKDWHLSTG FLGTPRLLPV LTDTGHTDVA YRLLHQRTFP SWGYPIDKGS TTMWERWDSI
QPDGGFQTPE MNSFNHYAYG SVGEWMYANI AGIAPGRAGY RQVVIRPRPG GEVTSARATF
ASLHGPVSTR WQQRSGGFVL TCSVPPNTTA EVWIPADHPD RVQHTHGTFV RAEDGCAVFE
VGSGSHRFTV
