DDRB_KLEOK
ID DDRB_KLEOK Reviewed; 125 AA.
AC O68196; A0A0H3H783;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 85.
DE RecName: Full=Diol dehydratase-reactivating factor small subunit {ECO:0000303|PubMed:9405397};
DE Short=DDR small subunit;
DE AltName: Full=Diol dehydratase-reactivase small subunit {ECO:0000303|PubMed:21040475};
DE AltName: Full=Diol dehydratase-reactivating factor beta subunit {ECO:0000303|PubMed:16338403};
DE Short=DDR beta subunit;
DE Short=DDRB;
GN Name=ddrB {ECO:0000303|PubMed:9405397};
GN Synonyms=pduH {ECO:0000303|PubMed:22493189}; OrderedLocusNames=KOX_01475;
OS Klebsiella oxytoca (strain ATCC 8724 / DSM 4798 / JCM 20051 / NBRC 3318 /
OS NRRL B-199 / KCTC 1686 / BUCSAV 143 / CCM 1901).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX NCBI_TaxID=1006551;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION OF
RP DDR COMPLEX, AND SUBUNIT.
RC STRAIN=ATCC 8724 / DSM 4798 / JCM 20051 / NBRC 3318 / NRRL B-199 / KCTC
RC 1686 / BUCSAV 143 / CCM 1901;
RX PubMed=9405397; DOI=10.1074/jbc.272.51.32034;
RA Mori K., Tobimatsu T., Hara T., Toraya T.;
RT "Characterization, sequencing, and expression of the genes encoding a
RT reactivating factor for glycerol-inactivated adenosylcobalamin-dependent
RT diol dehydratase.";
RL J. Biol. Chem. 272:32034-32041(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 8724 / DSM 4798 / JCM 20051 / NBRC 3318 / NRRL B-199 / KCTC
RC 1686 / BUCSAV 143 / CCM 1901;
RX PubMed=22493189; DOI=10.1128/jb.00026-12;
RA Shin S.H., Kim S., Kim J.Y., Lee S., Um Y., Oh M.K., Kim Y.R., Lee J.,
RA Yang K.S.;
RT "Complete genome sequence of Klebsiella oxytoca KCTC 1686, used in
RT production of 2,3-butanediol.";
RL J. Bacteriol. 194:2371-2372(2012).
RN [3]
RP PROTEIN SEQUENCE OF 1-10, FUNCTION OF DDR COMPLEX, AND SUBUNIT.
RC STRAIN=ATCC 8724 / DSM 4798 / JCM 20051 / NBRC 3318 / NRRL B-199 / KCTC
RC 1686 / BUCSAV 143 / CCM 1901;
RX PubMed=9920879; DOI=10.1074/jbc.274.6.3372;
RA Toraya T., Mori K.;
RT "A reactivating factor for coenzyme B12-dependent diol dehydratase.";
RL J. Biol. Chem. 274:3372-3377(1999).
RN [4]
RP FUNCTION OF DDR COMPLEX, REACTION MECHANISM, INTERACTION OF DDR COMPLEX
RP WITH DIOL DEHYDRATASE, AND ATPASE ACTIVITY OF DDR COMPLEX.
RC STRAIN=ATCC 8724 / DSM 4798 / JCM 20051 / NBRC 3318 / NRRL B-199 / KCTC
RC 1686 / BUCSAV 143 / CCM 1901;
RX PubMed=10529189; DOI=10.1021/bi9911738;
RA Mori K., Toraya T.;
RT "Mechanism of reactivation of coenzyme B12-dependent diol dehydratase by a
RT molecular chaperone-like reactivating factor.";
RL Biochemistry 38:13170-13178(1999).
RN [5]
RP FUNCTION OF DDR COMPLEX, SUBUNIT, AND SUBSTRATE SPECIFICITY OF DDR COMPLEX.
RX PubMed=17916188; DOI=10.1111/j.1742-4658.2007.06074.x;
RA Kajiura H., Mori K., Shibata N., Toraya T.;
RT "Molecular basis for specificities of reactivating factors for
RT adenosylcobalamin-dependent diol and glycerol dehydratases.";
RL FEBS J. 274:5556-5566(2007).
RN [6]
RP FUNCTION OF DDR COMPLEX.
RX PubMed=18586770; DOI=10.1093/jb/mvn086;
RA Toraya T., Tamura N., Watanabe T., Yamanishi M., Hieda N., Mori K.;
RT "Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by
RT 3-unsaturated 1,2-diols and thioglycerol.";
RL J. Biochem. 144:437-446(2008).
RN [7]
RP FUNCTION OF DDR COMPLEX, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP INTERACTION WITH DDRB AND DIOL DEHYDRATASE.
RX PubMed=21040475; DOI=10.1111/j.1742-4658.2010.07898.x;
RA Mori K., Hosokawa Y., Yoshinaga T., Toraya T.;
RT "Diol dehydratase-reactivating factor is a reactivase--evidence for
RT multiple turnovers and subunit swapping with diol dehydratase.";
RL FEBS J. 277:4931-4943(2010).
RN [8] {ECO:0007744|PDB:2D0O, ECO:0007744|PDB:2D0P}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH DRRA AND MAGNESIUM,
RP AND COFACTOR.
RX PubMed=16338403; DOI=10.1016/j.str.2005.08.011;
RA Shibata N., Mori K., Hieda N., Higuchi Y., Yamanishi M., Toraya T.;
RT "Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray
RT structures of diol dehydratase-reactivating factor.";
RL Structure 13:1745-1754(2005).
CC -!- FUNCTION: Small subunit of the diol dehydratase-reactivating factor
CC (DDR), which reactivates suicidally inhibited adenosylcobalamin-
CC dependent diol dehydratase (DD, pddA, pddB, pddC). DDR acts as a
CC chaperone, reactivates inactivated DD holoenzyme in the presence of
CC ATP, Mg(2+) and free adenosylcobalamin (AdoCbl), by mediating the
CC exchange of the tightly bound damaged cofactor AdoCbl for a free intact
CC one (PubMed:9405397, PubMed:9920879, PubMed:10529189, PubMed:17916188,
CC PubMed:18586770, PubMed:21040475). Reactivation takes place in two
CC steps: ADP-dependent cobalamin release, and ATP-dependent dissociation
CC of the DD apoenzyme-DDR complex. DDR has weak ATPase activity which is
CC required for DD reactivation (PubMed:10529189, PubMed:17916188,
CC PubMed:21040475). Activates glycerol-inactivated, O2-inactivated
CC holoenzyme and inactivated enzyme-cyanocobalamin complex
CC (PubMed:9920879). Also reactivates glycerol-inactivated hologlycerol
CC dehydratase, a DD isozyme (PubMed:17916188).
CC {ECO:0000269|PubMed:10529189, ECO:0000269|PubMed:17916188,
CC ECO:0000269|PubMed:18586770, ECO:0000269|PubMed:21040475,
CC ECO:0000269|PubMed:9405397, ECO:0000269|PubMed:9920879}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000269|PubMed:10529189, ECO:0000269|PubMed:21040475};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16338403, ECO:0000269|PubMed:21040475};
CC Note=One Mg(2+)is bound by the enzyme, a second binds only to the beta-
CC phosphate of DdrA-bound ADP (PubMed:16338403). Co(2+), Mn(2+) and
CC Ni(2+) can substitute in vitro (PubMed:21040475).
CC {ECO:0000269|PubMed:16338403, ECO:0000269|PubMed:21040475};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.9 mM for ATP, during activation and reactivation of glycerol-
CC inactivated holoenzyme or enzyme-CN-Cbl complex
CC {ECO:0000269|PubMed:21040475};
CC Note=kcat for enzyme-bound damaged AdoCbl is 0.14 min(-1), kcat for
CC reactivation of CN-Cbl-inactivated enzyme is 0.27 min(-1).
CC {ECO:0000269|PubMed:21040475};
CC -!- SUBUNIT: Component of the DDR complex, a heterotetramer of
CC DdrA(2)/DdrB(2) (Probable) (PubMed:9920879, PubMed:10529189,
CC PubMed:16338403, PubMed:17916188, PubMed:21040475). The DDR complex
CC interacts with the diol dehydratase complex in the presence of ADP but
CC not ATP (PubMed:10529189, PubMed:21040475).
CC {ECO:0000269|PubMed:10529189, ECO:0000269|PubMed:16338403,
CC ECO:0000269|PubMed:17916188, ECO:0000269|PubMed:21040475,
CC ECO:0000269|PubMed:9920879, ECO:0000305|PubMed:9405397}.
CC -!- INTERACTION:
CC O68196; O68195: ddrA; Xeno; NbExp=4; IntAct=EBI-8491890, EBI-8491873;
CC -!- SIMILARITY: Belongs to the DdrB/PduH family. {ECO:0000305}.
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DR EMBL; AF017781; AAC15872.1; -; Genomic_DNA.
DR EMBL; CP003218; AEX02040.1; -; Genomic_DNA.
DR PIR; T08598; T08598.
DR RefSeq; WP_014226639.1; NZ_PQKQ01000004.1.
DR PDB; 2D0O; X-ray; 2.00 A; B/D=1-125.
DR PDB; 2D0P; X-ray; 3.00 A; B/D=1-125.
DR PDBsum; 2D0O; -.
DR PDBsum; 2D0P; -.
DR SMR; O68196; -.
DR DIP; DIP-48461N; -.
DR IntAct; O68196; 1.
DR MINT; O68196; -.
DR EnsemblBacteria; AEX02040; AEX02040; KOX_01475.
DR EnsemblBacteria; SAQ35413; SAQ35413; SAMEA2273883_02669.
DR KEGG; kox:KOX_01475; -.
DR PATRIC; fig|1006551.4.peg.298; -.
DR HOGENOM; CLU_139758_2_0_6; -.
DR OMA; AHRNTGN; -.
DR EvolutionaryTrace; O68196; -.
DR PRO; PR:O68196; -.
DR Proteomes; UP000007843; Chromosome.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.10150; -; 1.
DR InterPro; IPR010254; B12-dep_deHydtase_bsu.
DR InterPro; IPR003208; Dehydtase/Dehydtase_re.
DR InterPro; IPR009192; Diol/glycerol_deHydtase_re_ssu.
DR Pfam; PF02288; Dehydratase_MU; 1.
DR PIRSF; PIRSF011503; DdrB_PduH; 1.
DR SUPFAM; SSF52968; SSF52968; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chaperone; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding.
FT CHAIN 1..125
FT /note="Diol dehydratase-reactivating factor small subunit"
FT /id="PRO_0000454162"
FT BINDING 31
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16338403,
FT ECO:0007744|PDB:2D0O"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 19..22
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 23..31
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 46..55
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 67..74
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 92..106
FT /evidence="ECO:0007829|PDB:2D0O"
SQ SEQUENCE 125 AA; 13620 MW; 8EC5E809C59EF74C CRC64;
MNGNHSAPAI AIAVIDGCDG LWREVLLGIE EEGIPFRLQH HPAGEVVDSA WQAARSSPLL
VGIACDRHML VVHYKNLPAS APLFTLMHHQ DSQAHRNTGN NAARLVKGIP FRDLNSEATG
EQQDE
