3XYN1_VIBSX
ID 3XYN1_VIBSX Reviewed; 576 AA.
AC D5MP61;
DT 11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 1.
DT 25-MAY-2022, entry version 32.
DE RecName: Full=Beta-1,3-xylanase XYL4 {ECO:0000303|PubMed:19605459};
DE EC=3.2.1.32;
DE AltName: Full=Beta-1,3-xylanase {ECO:0000312|EMBL:BAD51934.1};
DE Flags: Precursor;
GN Name=xyl4 {ECO:0000312|EMBL:BAD51934.1};
OS Vibrio sp.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=678;
RN [1] {ECO:0000305, ECO:0000312|EMBL:BAD51934.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF GLU-138;
RP GLU-234 AND GLU-268.
RC STRAIN=AX-4 {ECO:0000312|EMBL:BAD51934.1};
RX PubMed=15743273; DOI=10.1042/bj20050190;
RA Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Nakamura T., Ito M.;
RT "Molecular cloning and characterization of a novel beta-1,3-xylanase
RT possessing two putative carbohydrate-binding modules from a marine
RT bacterium Vibrio sp. strain AX-4.";
RL Biochem. J. 388:949-957(2005).
RN [2] {ECO:0000305}
RP CBM31 DOMAIN.
RC STRAIN=AX-4 {ECO:0000269|PubMed:19605459};
RX PubMed=19605459; DOI=10.1093/jb/mvp108;
RA Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Ito M.;
RT "Characterization and application of carbohydrate-binding modules of beta-
RT 1,3-xylanase XYL4.";
RL J. Biochem. 146:633-641(2009).
RN [3] {ECO:0000305}
RP X-RAY CRYSTALLOGRAPHY (0.86 ANGSTROMS) OF 23-349 IN COMPLEX WITH MAGNESIUM.
RC STRAIN=AX-4 {ECO:0000269|Ref.3};
RA Sakaguchi K., Kawamura T., Watanabe N., Kiyohara M., Yamaguchi K., Ito M.,
RA Tanaka I.;
RT "Atomic resolution analysis of beta-1,3-xylanase catalytic module from
RT Vibrio sp. AX-4.";
RL Submitted (FEB-2006) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the hydrolysis of beta-1,3-xylan into
CC oligosaccharides, mainly xylobiose, xylotriose and xylotetraose.
CC Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-
CC 1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-
CC xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-
CC 1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-
CC nitrophenyl-beta-xyloside. {ECO:0000269|PubMed:15743273}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Random hydrolysis of (1->3)-beta-D-glycosidic linkages in
CC (1->3)-beta-D-xylans.; EC=3.2.1.32;
CC Evidence={ECO:0000269|PubMed:15743273};
CC -!- ACTIVITY REGULATION: Completely inhibited by Hg(2+), partially
CC inhibited by Mn(2+), Cu(2+) and Pb(2+). Unaffected by Ca(2+), Mg(2+)
CC and EDTA. {ECO:0000269|PubMed:15743273}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.4 mM for beta-1,3-xylotetraose {ECO:0000269|PubMed:15743273};
CC KM=7.5 mM for beta-1,3-xylopentaose {ECO:0000269|PubMed:15743273};
CC pH dependence:
CC Optimum pH is 7.0-7.5. {ECO:0000269|PubMed:15743273};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius. Inactive above 60 degrees
CC Celsius. {ECO:0000269|PubMed:15743273};
CC -!- DOMAIN: The carbohydrate binding modules (CBM) bind to insoluble beta-
CC 1,3-xylan, but not to insoluble beta-1,4-xylan, beta-1,4-glucan, beta-
CC 1,4-mannan, curdlan, chitin, or soluble polysaccharides.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 26 family.
CC {ECO:0000255|PROSITE-ProRule:PRU01100, ECO:0000269|PubMed:15743273}.
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DR EMBL; AB121027; BAD51934.1; -; Genomic_DNA.
DR PDB; 2DDX; X-ray; 0.86 A; A=23-349.
DR PDB; 3VPL; X-ray; 1.20 A; A=23-349.
DR PDBsum; 2DDX; -.
DR PDBsum; 3VPL; -.
DR AlphaFoldDB; D5MP61; -.
DR SMR; D5MP61; -.
DR BRENDA; 3.2.1.32; 6640.
DR EvolutionaryTrace; D5MP61; -.
DR GO; GO:0030247; F:polysaccharide binding; IDA:UniProtKB.
DR GO; GO:0033905; F:xylan endo-1,3-beta-xylosidase activity; IDA:UniProtKB.
DR GO; GO:0030245; P:cellulose catabolic process; IEA:UniProtKB-KW.
DR GO; GO:0045493; P:xylan catabolic process; IDA:UniProtKB.
DR Gene3D; 2.60.40.2450; -; 2.
DR InterPro; IPR021016; Beta-xylanase.
DR InterPro; IPR038560; Beta-xylanase_CBM31_sf.
DR InterPro; IPR022790; GH26_dom.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR Pfam; PF11606; AlcCBM31; 2.
DR SUPFAM; SSF51445; SSF51445; 1.
DR PROSITE; PS51764; GH26; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Cellulose degradation;
KW Disulfide bond; Glycosidase; Hydrolase; Polysaccharide degradation; Repeat;
KW Signal; Xylan degradation.
FT SIGNAL 1..22
FT /evidence="ECO:0000255"
FT CHAIN 23..576
FT /note="Beta-1,3-xylanase XYL4"
FT /evidence="ECO:0000255"
FT /id="PRO_0000403220"
FT DOMAIN 23..293
FT /note="GH26"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01100"
FT REGION 347..367
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 363..453
FT /note="Carbohydrate binding module (CBM) 1"
FT REGION 450..486
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 487..574
FT /note="Carbohydrate binding module (CBM) 2"
FT ACT_SITE 138
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01100"
FT ACT_SITE 234
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01100"
FT DISULFID 368..452
FT /evidence="ECO:0000250|UniProtKB:Q8RS40"
FT DISULFID 399..404
FT /evidence="ECO:0000250|UniProtKB:Q8RS40"
FT DISULFID 490..574
FT /evidence="ECO:0000250|UniProtKB:Q8RS40"
FT DISULFID 521..526
FT /evidence="ECO:0000250|UniProtKB:Q8RS40"
FT MUTAGEN 138
FT /note="E->D: Very low catalytic activity."
FT /evidence="ECO:0000269|PubMed:15743273"
FT MUTAGEN 138
FT /note="E->Q: Complete loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:15743273"
FT MUTAGEN 234
FT /note="E->D: Very low catalytic activity."
FT /evidence="ECO:0000269|PubMed:15743273"
FT MUTAGEN 234
FT /note="E->Q: Complete loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:15743273"
FT MUTAGEN 268
FT /note="E->Q: Catalytic activity reduced by 30%."
FT /evidence="ECO:0000269|PubMed:15743273"
FT TURN 24..27
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 30..40
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 83..89
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 93..100
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 105..109
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 110..113
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 114..125
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 148..165
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 168..170
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 171..176
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 199..207
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 208..211
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 214..226
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 230..235
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 242..245
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 251..253
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 262..268
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 270..279
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 280..283
FT /evidence="ECO:0007829|PDB:2DDX"
FT STRAND 284..290
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 294..296
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:2DDX"
FT TURN 302..306
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 318..328
FT /evidence="ECO:0007829|PDB:2DDX"
FT HELIX 340..343
FT /evidence="ECO:0007829|PDB:2DDX"
SQ SEQUENCE 576 AA; 62591 MW; E04449C5F703884D CRC64;
MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA LGTIPAGVTN
YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS MNGEVDAVAS GRYNANIDTL
LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG IVTSFQYVHD RIIALGHQAK ISLVWQVASY
CPTPGGQLDQ WWPGSEYVDW VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY
QVADLTYSAD PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW
AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG GGDNGGGDNG
GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL NGLCLQGEIK NGEYVKQFDA
QLGSTYGIEF KVADGESQFI TDKSVTFENK QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG
SGGGTDPSQC SADFGYNYRS DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF
NATLGSDYKI TFKVEDSASQ FITEKNITFV NTSCAQ
