ARAD_RHILW
ID ARAD_RHILW Reviewed; 579 AA.
AC B5ZZ34;
DT 11-DEC-2019, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=L-arabinonate dehydratase {ECO:0000305};
DE Short=ArDHT {ECO:0000303|PubMed:27102126};
DE EC=4.2.1.25 {ECO:0000269|PubMed:27102126};
DE AltName: Full=D-fuconate dehydratase {ECO:0000305};
DE EC=4.2.1.67 {ECO:0000269|PubMed:27102126};
DE AltName: Full=Galactonate dehydratase {ECO:0000305};
DE EC=4.2.1.6 {ECO:0000269|PubMed:27102126};
DE AltName: Full=L-arabonate dehydratase {ECO:0000303|PubMed:27102126};
GN Name=araD {ECO:0000303|PubMed:27102126};
GN OrderedLocusNames=Rleg2_2909 {ECO:0000312|EMBL:ACI56177.1};
OS Rhizobium leguminosarum bv. trifolii (strain WSM2304).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX NCBI_TaxID=395492;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=WSM2304;
RX PubMed=21304679; DOI=10.4056/sigs.44642;
RA Reeve W., O'Hara G., Chain P., Ardley J., Brau L., Nandesena K., Tiwari R.,
RA Malfatti S., Kiss H., Lapidus A., Copeland A., Nolan M., Land M.,
RA Ivanova N., Mavromatis K., Markowitz V., Kyrpides N., Melino V., Denton M.,
RA Yates R., Howieson J.;
RT "Complete genome sequence of Rhizobium leguminosarum bv trifolii strain
RT WSM2304, an effective microsymbiont of the South American clover Trifolium
RT polymorphum.";
RL Stand. Genomic Sci. 2:66-76(2010).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, IRON-SULFUR CLUSTER,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF CYS-59; CYS-127;
RP CYS-200; CYS-436 AND CYS-443.
RX PubMed=27102126; DOI=10.1007/s00253-016-7530-8;
RA Andberg M., Aro-Kaerkkaeinen N., Carlson P., Oja M., Bozonnet S.,
RA Toivari M., Hakulinen N., O'Donohue M., Penttilae M., Koivula A.;
RT "Characterization and mutagenesis of two novel iron-sulphur cluster
RT pentonate dehydratases.";
RL Appl. Microbiol. Biotechnol. 100:7549-7563(2016).
RN [3]
RP CRYSTALLIZATION.
RX PubMed=27487924; DOI=10.1107/s2053230x16010311;
RA Rahman M.M., Andberg M., Koivula A., Rouvinen J., Hakulinen N.;
RT "Crystallization and X-ray diffraction analysis of an L-arabinonate
RT dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate
RT dehydratase from Caulobacter crescentus.";
RL Acta Crystallogr. F Struct. Biol. Commun. 72:604-608(2016).
RN [4] {ECO:0007744|PDB:5J83, ECO:0007744|PDB:5J84, ECO:0007744|PDB:5J85}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 2-579 OF APOENZYME; IN COMPLEX
RP WITH 2FE-2S AND MAGNESIUM AND OF MUTANT ALA-480, COFACTOR, SUBUNIT, AND
RP MUTAGENESIS OF SER-480.
RX PubMed=28574691; DOI=10.1021/acschembio.7b00304;
RA Rahman M.M., Andberg M., Thangaraj S.K., Parkkinen T., Penttila M.,
RA Janis J., Koivula A., Rouvinen J., Hakulinen N.;
RT "The crystal structure of a bacterial L-arabinonate dehydratase contains a
RT [2Fe-2S] cluster.";
RL ACS Chem. Biol. 12:1919-1927(2017).
CC -!- FUNCTION: Catalyzes the dehydration of L-arabinonate to 2-dehydro-3-
CC deoxy-L-arabinonate during L-arabinose degradation. Can also dehydrate
CC D-galactonate and D-fuconate with good catalytic efficiency. Has weak
CC activity with D-xylonate and D-gluconate.
CC {ECO:0000269|PubMed:27102126}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O;
CC Xref=Rhea:RHEA:20968, ChEBI:CHEBI:15377, ChEBI:CHEBI:16501,
CC ChEBI:CHEBI:35173; EC=4.2.1.25;
CC Evidence={ECO:0000269|PubMed:27102126};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O;
CC Xref=Rhea:RHEA:18649, ChEBI:CHEBI:12931, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57989; EC=4.2.1.6;
CC Evidence={ECO:0000269|PubMed:27102126};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H2O;
CC Xref=Rhea:RHEA:12949, ChEBI:CHEBI:15377, ChEBI:CHEBI:35372,
CC ChEBI:CHEBI:58378; EC=4.2.1.67;
CC Evidence={ECO:0000269|PubMed:27102126};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:28574691, ECO:0000305|PubMed:27102126};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27102126, ECO:0000269|PubMed:28574691};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.8 mM for L-arabinonate {ECO:0000269|PubMed:27102126};
CC KM=3.8 mM for D-galactonate {ECO:0000269|PubMed:27102126};
CC KM=1.8 mM for D-fuconate {ECO:0000269|PubMed:27102126};
CC KM=9.2 mM for D-xylonate {ECO:0000269|PubMed:27102126};
CC KM=11.9 mM for D-gluconate {ECO:0000269|PubMed:27102126};
CC Note=kcat is 728 min(-1) with L-arabinonate as substrate. kcat is
CC 1377 min(-1) with D-galactonate as substrate. kcat is 2949 min(-1)
CC with D-fuconate as substrate. kcat is 349 min(-1) with D-xylonate as
CC substrate. kcat is 431 min(-1) with D-gluconate as substrate.
CC {ECO:0000269|PubMed:27102126};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:27102126};
CC -!- PATHWAY: Carbohydrate metabolism. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:27102126,
CC ECO:0000269|PubMed:28574691}.
CC -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000305}.
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DR EMBL; CP001191; ACI56177.1; -; Genomic_DNA.
DR RefSeq; WP_003592857.1; NC_011369.1.
DR PDB; 5J83; X-ray; 3.00 A; A/B=2-579.
DR PDB; 5J84; X-ray; 2.40 A; A/B/C/D/E/F/G/H=2-579.
DR PDB; 5J85; X-ray; 2.60 A; A=2-579.
DR PDBsum; 5J83; -.
DR PDBsum; 5J84; -.
DR PDBsum; 5J85; -.
DR AlphaFoldDB; B5ZZ34; -.
DR SMR; B5ZZ34; -.
DR STRING; 395492.Rleg2_2909; -.
DR EnsemblBacteria; ACI56177; ACI56177; Rleg2_2909.
DR KEGG; rlt:Rleg2_2909; -.
DR eggNOG; COG0129; Bacteria.
DR HOGENOM; CLU_014271_3_1_5; -.
DR OMA; GSCMTMG; -.
DR OrthoDB; 193579at2; -.
DR Proteomes; UP000008330; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0047818; F:D-fuconate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0008869; F:galactonate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0050020; F:L-arabinonate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019568; P:arabinose catabolic process; IEA:UniProtKB-KW.
DR Gene3D; 3.50.30.80; -; 1.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR037237; IlvD/EDD_N.
DR Pfam; PF00920; ILVD_EDD; 1.
DR SUPFAM; SSF143975; SSF143975; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Arabinose catabolism; Carbohydrate metabolism; Iron;
KW Iron-sulfur; Lyase; Magnesium; Metal-binding.
FT CHAIN 1..579
FT /note="L-arabinonate dehydratase"
FT /id="PRO_0000448799"
FT BINDING 59
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:28574691"
FT BINDING 91
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:28574691"
FT BINDING 127
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:28574691"
FT BINDING 128
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:28574691"
FT BINDING 200
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:28574691"
FT BINDING 453
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:28574691"
FT MUTAGEN 59
FT /note="C->S: Loss of activity. Does not bind iron-sulfur
FT cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 127
FT /note="C->S: Loss of activity. Does not bind iron-sulfur
FT cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 200
FT /note="C->S: Almost loss of activity. Does not bind iron-
FT sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 436
FT /note="C->S: No change in activity. Does not affect binding
FT of iron-sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 443
FT /note="C->S: Slight decrease in activity. Does not affect
FT binding of iron-sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 480
FT /note="S->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28574691"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 18..21
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 22..31
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 38..41
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 63..76
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 80..85
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 91..93
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 98..101
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 102..114
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 130..139
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 156..163
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 167..177
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 183..189
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 190..192
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 205..215
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 221..225
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 231..250
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 254..257
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 260..273
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 278..290
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 296..303
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 320..326
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 329..338
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 354..358
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 366..368
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 372..374
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 376..379
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 383..389
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 393..396
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 398..400
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 406..417
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 418..424
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 436..440
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 445..449
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 461..464
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 465..467
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 473..477
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 485..493
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 495..497
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 500..503
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 509..513
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 514..517
FT /evidence="ECO:0007829|PDB:5J84"
FT STRAND 518..521
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 525..533
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 545..553
FT /evidence="ECO:0007829|PDB:5J84"
FT TURN 557..560
FT /evidence="ECO:0007829|PDB:5J84"
FT HELIX 564..566
FT /evidence="ECO:0007829|PDB:5J84"
SQ SEQUENCE 579 AA; 62583 MW; A142C250B304F3C3 CRC64;
MKKKAEWPRK LRSQEWYGGT SRDVIYHRGW LKNQGYPHDL FDGRPVIGIL NTWSDMTPCN
GHLRELAEKV KAGVWEAGGF PLEVPVFSAS ENTFRPTAMM YRNLAALAVE EAIRGQPMDG
CVLLVGCDKT TPSLLMGAAS CDLPSIVVTG GPMLNGYFRG ERVGSGTHLW KFSEMVKAGE
MTQAEFLEAE ASMSRSSGTC NTMGTASTMA SMAEALGMAL SGNAAIPGVD SRRKVMAQLT
GRRIVQMVKD DLKPSEIMTK QAFENAIRTN AAIGGSTNAV IHLLAIAGRV GIDLSLDDWD
RCGRDVPTIV NLMPSGKYLM EEFFYAGGLP VVLKRLGEAG LLHKDALTVS GETVWDEVKD
VVNWNEDVIL PAEKALTSSG GIVVLRGNLA PKGAVLKPSA ASPHLLVHKG RAVVFEDIDD
YKAKINDDNL DIDENCIMVM KNCGPKGYPG MAEVGNMGLP PKVLKKGILD MVRISDARMS
GTAYGTVVLH TSPEAAVGGP LAVVKNGDMI ELDVPNRRLH LDISDEELAR RLAEWQPNHD
LPTSGYAFLH QQHVEGADTG ADLDFLKGCR GNAVGKDSH
