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Exo-oligoalginate lyase (EC 4.2.2.26) (Exo-type alginate lyase) (Exolytic alginate lyase)

 EALGL_SACD2             Reviewed;         736 AA.
Q21FJ0;
11-MAY-2016, integrated into UniProtKB/Swiss-Prot.
18-APR-2006, sequence version 1.
28-FEB-2018, entry version 70.
RecName: Full=Exo-oligoalginate lyase {ECO:0000303|PubMed:22281843};
EC=4.2.2.26 {ECO:0000269|PubMed:22281843, ECO:0000269|PubMed:24478312};
AltName: Full=Exo-type alginate lyase {ECO:0000303|PubMed:22281843};
AltName: Full=Exolytic alginate lyase {ECO:0000305};
Flags: Precursor;
Name=alg17C {ECO:0000303|PubMed:22281843};
Synonyms=alg17A {ECO:0000312|EMBL:ABD82539.1};
OrderedLocusNames=Sde_3284 {ECO:0000312|EMBL:ABD82539.1};
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024).
Bacteria; Proteobacteria; Gammaproteobacteria; Cellvibrionales;
Cellvibrionaceae; Saccharophagus.
NCBI_TaxID=203122;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=2-40 / ATCC 43961 / DSM 17024;
PubMed=18516288; DOI=10.1371/journal.pgen.1000087;
Weiner R.M., Taylor L.E. II, Henrissat B., Hauser L., Land M.,
Coutinho P.M., Rancurel C., Saunders E.H., Longmire A.G., Zhang H.,
Bayer E.A., Gilbert H.J., Larimer F., Zhulin I.B., Ekborg N.A.,
Lamed R., Richardson P.M., Borovok I., Hutcheson S.;
"Complete genome sequence of the complex carbohydrate-degrading marine
bacterium, Saccharophagus degradans strain 2-40 T.";
PLoS Genet. 4:E1000087-E1000087(2008).
[2]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
BIOTECHNOLOGY.
STRAIN=2-40 / ATCC 43961 / DSM 17024;
PubMed=22281843; DOI=10.1007/s00253-012-3882-x;
Kim H.T., Chung J.H., Wang D., Lee J., Woo H.C., Choi I.G., Kim K.H.;
"Depolymerization of alginate into a monomeric sugar acid using
Alg17C, an exo-oligoalginate lyase cloned from Saccharophagus
degradans 2-40.";
Appl. Microbiol. Biotechnol. 93:2233-2239(2012).
[3]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 24-736 OF WILD-TYPE AND
MUTANTS LEU-202 AND ALA-258 IN COMPLEX WITH ZINC AND A TRISACCHARIDE
SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
PROPERTIES, COFACTOR, SUBUNIT, MUTAGENESIS OF ASN-149; ASN-201;
HIS-202; TYR-258; ARG-260; HIS-415; ARG-438 AND TYR-450, REACTION
MECHANISM, AND ACTIVE SITE.
STRAIN=2-40 / ATCC 43961 / DSM 17024;
PubMed=24478312; DOI=10.1074/jbc.M113.531111;
Park D., Jagtap S., Nair S.K.;
"Structure of a PL17 family alginate lyase demonstrates functional
similarities among exotype depolymerases.";
J. Biol. Chem. 289:8645-8655(2014).
-!- FUNCTION: Catalyzes the depolymerization of alginate through an
exolytic mode of action, via a beta-elimination mechanism.
Preferentially acts on oligoalginates with degrees of
polymerization higher than 2 to produce the alginate monomer, 4-
deoxy-L-erythro-5-hexoseulose uronic acid.
{ECO:0000269|PubMed:22281843, ECO:0000269|PubMed:24478312}.
-!- CATALYTIC ACTIVITY: Cleavage of 4-deoxy-alpha-L-erythro-hex-4-
enopyranuronoside oligosaccharides into 4-deoxy-alpha-L-erythro-
hex-4-enopyranuronate monosaccharides.
{ECO:0000269|PubMed:22281843, ECO:0000269|PubMed:24478312}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:24478312};
Note=The zinc ion seen in the crystal structure is located far
away from the active site and likely plays a structural role.
However, it seems important for enzyme activity since the mutation
of one of its coordination residues causes a high decrease in
activity. {ECO:0000269|PubMed:24478312};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=35.2 mg/ml for alginate (at pH 6 and 40 degrees Celsius)
{ECO:0000269|PubMed:22281843};
KM=22.3 uM for low viscosity alginate (at pH 7.5 and 30 degrees
Celsius) {ECO:0000269|PubMed:24478312};
KM=7.7 uM for alginate trisaccharide (at pH 7.5 and 30 degrees
Celsius) {ECO:0000269|PubMed:24478312};
Vmax=41.7 umol/min/mg enzyme with alginate as substrate (at pH 6
and 40 degrees Celsius) {ECO:0000269|PubMed:22281843};
Note=kcat is 56.9 sec(-1) with low viscosity alginate as
substrate. kcat is 62.4 sec(-1) with alginate trisaccharide as
substrate (at pH 7.5 and 30 degrees Celsius).
{ECO:0000269|PubMed:24478312};
pH dependence:
Optimum pH is 6. {ECO:0000269|PubMed:22281843};
Temperature dependence:
Optimum temperature is 40 degrees Celsius.
{ECO:0000269|PubMed:22281843};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24478312}.
-!- SUBCELLULAR LOCATION: Periplasm {ECO:0000305}.
-!- BIOTECHNOLOGY: Could be used as the key enzyme to produce alginate
monomers in the process of utilizing alginate for biofuels and
chemicals production. {ECO:0000305|PubMed:22281843}.
-!- SIMILARITY: Belongs to the polysaccharide lyase 17 family.
{ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; CP000282; ABD82539.1; -; Genomic_DNA.
RefSeq; WP_011469755.1; NC_007912.1.
PDB; 4NEI; X-ray; 1.85 A; A/B=1-736.
PDB; 4OJZ; X-ray; 1.90 A; A/B=1-736.
PDB; 4OK2; X-ray; 2.45 A; A/B=1-736.
PDB; 4OK4; X-ray; 1.70 A; A/B=1-736.
PDBsum; 4NEI; -.
PDBsum; 4OJZ; -.
PDBsum; 4OK2; -.
PDBsum; 4OK4; -.
SMR; Q21FJ0; -.
STRING; 203122.Sde_3284; -.
CAZy; PL17; Polysaccharide Lyase Family 17.
EnsemblBacteria; ABD82539; ABD82539; Sde_3284.
KEGG; sde:Sde_3284; -.
eggNOG; ENOG4105EY3; Bacteria.
eggNOG; ENOG410XRPE; LUCA.
HOGENOM; HOG000027047; -.
KO; K20525; -.
OMA; EGPYYQR; -.
OrthoDB; POG091H0H75; -.
BioCyc; SDEG203122:G1G67-3473-MONOMER; -.
Proteomes; UP000001947; Chromosome.
GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000272; P:polysaccharide catabolic process; IEA:UniProtKB-KW.
Gene3D; 1.50.10.100; -; 1.
InterPro; IPR008397; Alginate_lyase_dom.
InterPro; IPR008929; Chondroitin_lyas.
InterPro; IPR012480; Hepar_II_III.
Pfam; PF05426; Alginate_lyase; 1.
Pfam; PF07940; Hepar_II_III; 1.
SUPFAM; SSF48230; SSF48230; 1.
1: Evidence at protein level;
3D-structure; Carbohydrate metabolism; Complete proteome; Lyase;
Metal-binding; Periplasm; Polysaccharide degradation;
Reference proteome; Signal; Zinc.
SIGNAL 1 23 {ECO:0000255}.
CHAIN 24 736 Exo-oligoalginate lyase.
/FTId=PRO_5004200187.
REGION 146 149 Substrate binding. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
REGION 257 260 Substrate binding. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
ACT_SITE 258 258 Proton donor.
{ECO:0000305|PubMed:24478312}.
ACT_SITE 413 413 Proton acceptor.
{ECO:0000250|UniProtKB:B2FSW8}.
METAL 415 415 Zinc; via pros nitrogen.
{ECO:0000244|PDB:4NEI,
ECO:0000244|PDB:4OJZ,
ECO:0000244|PDB:4OK2,
ECO:0000244|PDB:4OK4,
ECO:0000269|PubMed:24478312}.
METAL 433 433 Zinc. {ECO:0000244|PDB:4NEI,
ECO:0000244|PDB:4OJZ,
ECO:0000244|PDB:4OK2,
ECO:0000244|PDB:4OK4,
ECO:0000269|PubMed:24478312}.
METAL 464 464 Zinc; via tele nitrogen.
{ECO:0000244|PDB:4NEI,
ECO:0000244|PDB:4OJZ,
ECO:0000244|PDB:4OK2,
ECO:0000244|PDB:4OK4,
ECO:0000269|PubMed:24478312}.
BINDING 136 136 Substrate. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
BINDING 198 198 Substrate. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
BINDING 202 202 Substrate. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
BINDING 438 438 Substrate. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
BINDING 667 667 Substrate. {ECO:0000244|PDB:4OJZ,
ECO:0000269|PubMed:24478312}.
SITE 201 201 Neutralizes the sugar carboxylate group
at subsite +1.
{ECO:0000305|PubMed:24478312}.
SITE 202 202 Neutralizes the sugar carboxylate group
at subsite +1.
{ECO:0000305|PubMed:24478312}.
MUTAGEN 149 149 N->A: 1600-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:24478312}.
MUTAGEN 201 201 N->A: Complete loss of catalytic
activity. {ECO:0000269|PubMed:24478312}.
MUTAGEN 202 202 H->L: 20-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:24478312}.
MUTAGEN 258 258 Y->A: Complete loss of catalytic
activity. {ECO:0000269|PubMed:24478312}.
MUTAGEN 260 260 R->A: 2000-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:24478312}.
MUTAGEN 415 415 H->A: 1000-fold decrease in catalytic
activity. {ECO:0000269|PubMed:24478312}.
MUTAGEN 438 438 R->A: 4400-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:24478312}.
MUTAGEN 450 450 Y->A: Complete loss of catalytic
activity. {ECO:0000269|PubMed:24478312}.
STRAND 32 36 {ECO:0000244|PDB:4OK4}.
HELIX 37 46 {ECO:0000244|PDB:4OK4}.
HELIX 47 49 {ECO:0000244|PDB:4OK4}.
HELIX 51 68 {ECO:0000244|PDB:4OK4}.
HELIX 84 106 {ECO:0000244|PDB:4OK4}.
HELIX 109 125 {ECO:0000244|PDB:4OK4}.
HELIX 126 128 {ECO:0000244|PDB:4OK4}.
STRAND 137 140 {ECO:0000244|PDB:4OJZ}.
STRAND 142 146 {ECO:0000244|PDB:4OK4}.
HELIX 147 162 {ECO:0000244|PDB:4OK4}.
HELIX 165 167 {ECO:0000244|PDB:4OK4}.
HELIX 170 179 {ECO:0000244|PDB:4OK4}.
HELIX 181 188 {ECO:0000244|PDB:4OK4}.
TURN 189 191 {ECO:0000244|PDB:4OK4}.
HELIX 193 196 {ECO:0000244|PDB:4OK4}.
HELIX 201 217 {ECO:0000244|PDB:4OK4}.
HELIX 220 228 {ECO:0000244|PDB:4OK4}.
STRAND 232 237 {ECO:0000244|PDB:4OK4}.
HELIX 238 244 {ECO:0000244|PDB:4OK4}.
HELIX 256 276 {ECO:0000244|PDB:4OK4}.
HELIX 278 280 {ECO:0000244|PDB:4OK4}.
TURN 282 284 {ECO:0000244|PDB:4OK4}.
HELIX 285 299 {ECO:0000244|PDB:4OK4}.
HELIX 321 334 {ECO:0000244|PDB:4OK4}.
HELIX 339 346 {ECO:0000244|PDB:4OK4}.
HELIX 353 363 {ECO:0000244|PDB:4OK4}.
STRAND 375 378 {ECO:0000244|PDB:4OK4}.
TURN 380 383 {ECO:0000244|PDB:4OJZ}.
STRAND 385 396 {ECO:0000244|PDB:4OK4}.
STRAND 400 407 {ECO:0000244|PDB:4OK4}.
HELIX 411 413 {ECO:0000244|PDB:4OK4}.
STRAND 420 425 {ECO:0000244|PDB:4OK4}.
STRAND 428 431 {ECO:0000244|PDB:4OK4}.
TURN 443 445 {ECO:0000244|PDB:4OK4}.
HELIX 446 448 {ECO:0000244|PDB:4OK4}.
HELIX 452 456 {ECO:0000244|PDB:4OK4}.
TURN 457 459 {ECO:0000244|PDB:4OK4}.
HELIX 461 463 {ECO:0000244|PDB:4OK4}.
STRAND 464 466 {ECO:0000244|PDB:4OK4}.
HELIX 474 477 {ECO:0000244|PDB:4OK4}.
HELIX 479 483 {ECO:0000244|PDB:4OK4}.
STRAND 488 494 {ECO:0000244|PDB:4OK4}.
STRAND 496 505 {ECO:0000244|PDB:4OK4}.
STRAND 507 509 {ECO:0000244|PDB:4OK4}.
STRAND 512 521 {ECO:0000244|PDB:4OK4}.
STRAND 526 528 {ECO:0000244|PDB:4OK4}.
STRAND 530 551 {ECO:0000244|PDB:4OK4}.
STRAND 553 560 {ECO:0000244|PDB:4OK4}.
STRAND 568 572 {ECO:0000244|PDB:4OK4}.
HELIX 578 580 {ECO:0000244|PDB:4OK4}.
STRAND 581 588 {ECO:0000244|PDB:4OK4}.
STRAND 594 600 {ECO:0000244|PDB:4OK4}.
STRAND 603 612 {ECO:0000244|PDB:4OK4}.
STRAND 618 625 {ECO:0000244|PDB:4OK4}.
STRAND 638 659 {ECO:0000244|PDB:4OK4}.
STRAND 661 663 {ECO:0000244|PDB:4OK4}.
TURN 664 667 {ECO:0000244|PDB:4OK4}.
STRAND 668 670 {ECO:0000244|PDB:4OK4}.
STRAND 675 684 {ECO:0000244|PDB:4OK4}.
STRAND 687 694 {ECO:0000244|PDB:4OK4}.
STRAND 699 704 {ECO:0000244|PDB:4OK4}.
STRAND 713 717 {ECO:0000244|PDB:4OK4}.
STRAND 719 732 {ECO:0000244|PDB:4OK4}.
SEQUENCE 736 AA; 81582 MW; 500D22ED19B8DB80 CRC64;
MLSVNTIKNT LLAAVLVSVP ATAQVSGNGH PNLIVTEQDV ANIAASWESY DAYAEQLNAD
KTNLDAFMAE GVVVPMPKDA GGGYTHEQHK RNYKAIRNAG FLYQVTGDEK YLTFAKDLLL
AYAKMYPSLG EHPNRKEQSP GRLFWQSLNE AVWLVYSIQG YDAIIDGLAA EEKQEIESGV
FLPMAKFLSV ESPETFNKIH NHGTWAVAAV GMTGYVLGND ELVEISLMGL DKTGKAGFMK
QLDKLFSPDG YYTEGPYYQR YALMPFIWFA KAIETNEPER KIFEYRNNIL LKAVYTTIDL
SYAGYFFPIN DALKDKGIDT VELVHALAIV YSITGDNTLL DIAQEQGRIS LTGDGLKVAK
AVGEGLTQPY NYRSILLGDG ADGDQGALSI HRLGEGHNHM ALVAKNTSQG MGHGHFDKLN
WLLYDNGNEI VTDYGAARYL NVEAKYGGHY LAENNTWAKQ TIAHNTLVVN EQSHFYGDVT
TADLHHPEVL SFYSGEDYQL SSAKEANAYD GVEFVRSMLL VNVPSLEHPI VVDVLNVSAD
KASTFDLPLY FNGQIIDFSF KVKDNKNVMK MLGKRNGYQH LWLRNTAPVG DASERATWIL
DDRFYSYAFV TSTPSKKQNV LIAELGANDP NYNLRQQQVL IRRVEKAKQA SFVSVLEPHG
KYDGSLETTS GAYSNVKSVK HVSENGKDVV VVDLKDGSNV VVALSYNANS EQVHKVNAGE
EAIEWKGFSS VVVRRK


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