DDRA_KLEOK
ID DDRA_KLEOK Reviewed; 610 AA.
AC O68195; G8WE31;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 82.
DE RecName: Full=Diol dehydratase-reactivating factor large subunit {ECO:0000303|PubMed:9405397};
DE Short=DDR large subunit;
DE AltName: Full=Diol dehydratase-reactivase large subunit {ECO:0000303|PubMed:21040475};
DE AltName: Full=Diol dehydratase-reactivating factor alpha subunit {ECO:0000303|PubMed:16338403};
DE Short=DDR alpha subunit;
DE Short=DDRA;
GN Name=ddrA {ECO:0000303|PubMed:9405397};
GN Synonyms=pduG {ECO:0000303|PubMed:22493189}; OrderedLocusNames=KOX_01470;
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 DDRB; ADP AND
RP MAGNESIUM, 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: Large 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, reactivating 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:10529189, PubMed:9405397, PubMed:9920879, PubMed:17916188,
CC PubMed:18586770, PubMed:21040475). Reactivation takes place in two
CC steps: ADP-dependent cobalamin release, then 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). This subunit contains the adenosine nucleotide
CC binding site (PubMed:16338403). Activates glycerol-inactivated, O2-
CC inactivated 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:16338403,
CC ECO:0000269|PubMed:17916188, ECO:0000269|PubMed:18586770,
CC ECO:0000269|PubMed:21040475, ECO:0000269|PubMed:9405397,
CC 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 O68195; O68196: ddrB; Xeno; NbExp=4; IntAct=EBI-8491873, EBI-8491890;
CC -!- SIMILARITY: Belongs to the DdrA/PduG family. {ECO:0000305}.
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DR EMBL; AF017781; AAC15871.1; -; Genomic_DNA.
DR EMBL; CP003218; AEX02039.1; -; Genomic_DNA.
DR PIR; T08597; T08597.
DR RefSeq; WP_014226638.1; NC_016612.1.
DR PDB; 2D0O; X-ray; 2.00 A; A/C=1-610.
DR PDB; 2D0P; X-ray; 3.00 A; A/C=1-610.
DR PDBsum; 2D0O; -.
DR PDBsum; 2D0P; -.
DR AlphaFoldDB; O68195; -.
DR SMR; O68195; -.
DR DIP; DIP-48460N; -.
DR IntAct; O68195; 4.
DR MINT; O68195; -.
DR PRIDE; O68195; -.
DR EnsemblBacteria; AEX02039; AEX02039; KOX_01470.
DR GeneID; 66558084; -.
DR KEGG; kox:KOX_01470; -.
DR HOGENOM; CLU_449540_0_0_6; -.
DR OMA; LFHIRHE; -.
DR EvolutionaryTrace; O68195; -.
DR PRO; PR:O68195; -.
DR Proteomes; UP000007843; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.50.30.70; -; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR030994; DDR_dom.
DR InterPro; IPR040916; DDR_swiveling.
DR InterPro; IPR009191; DDRA.
DR InterPro; IPR028975; DDRA_swiveling_dom_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF08841; DDR; 1.
DR Pfam; PF18427; DDR_swiveling; 1.
DR PIRSF; PIRSF011502; DdrA_PduG; 1.
DR SUPFAM; SSF53067; SSF53067; 2.
DR SUPFAM; SSF82317; SSF82317; 1.
DR TIGRFAMs; TIGR04491; reactive_PduG; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Chaperone; Direct protein sequencing; Hydrolase;
KW Magnesium; Metal-binding; Nucleotide-binding.
FT CHAIN 1..610
FT /note="Diol dehydratase-reactivating factor large subunit"
FT /id="PRO_0000412975"
FT BINDING 11..13
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:2D0O"
FT BINDING 105
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16338403,
FT ECO:0007744|PDB:2D0O"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16338403,
FT ECO:0007744|PDB:2D0O"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16338403,
FT ECO:0007744|PDB:2D0O"
FT BINDING 459..462
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:2D0O"
FT BINDING 557..558
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:2D0O"
FT BINDING 591
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:2D0O"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 11..21
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 27..36
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 47..61
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 68..75
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 78..87
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 110..117
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 119..123
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 141..153
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 157..166
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 168..173
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 193..201
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 214..220
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 225..230
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 232..237
FT /evidence="ECO:0007829|PDB:2D0O"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 242..247
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 254..258
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 271..276
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 281..288
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 291..293
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 304..319
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 324..326
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 329..342
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 351..364
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 370..381
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 384..390
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 391..399
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 407..414
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 416..424
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 426..428
FT /evidence="ECO:0007829|PDB:2D0P"
FT STRAND 430..436
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 439..450
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 455..463
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 466..469
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 471..477
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 482..484
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 491..493
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 497..500
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 505..507
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 514..540
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 541..544
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 546..548
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 551..556
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 557..560
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 561..563
FT /evidence="ECO:0007829|PDB:2D0P"
FT HELIX 564..571
FT /evidence="ECO:0007829|PDB:2D0O"
FT TURN 572..574
FT /evidence="ECO:0007829|PDB:2D0O"
FT STRAND 578..581
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 584..586
FT /evidence="ECO:0007829|PDB:2D0O"
FT HELIX 593..605
FT /evidence="ECO:0007829|PDB:2D0O"
SQ SEQUENCE 610 AA; 64267 MW; B14C6DCBE13FA138 CRC64;
MRYIAGIDIG NSSTEVALAT LDEAGALTIT HSALAETTGI KGTLRNVFGI QEALALVARG
AGIAVSDISL IRINEATPVI GDVAMETITE TIITESTMIG HNPKTPGGAG LGTGITITPQ
ELLTRPADAP YILVVSSAFD FADIASVINA SLRAGYQITG VILQRDDGVL VSNRLEKPLP
IVDEVLYIDR IPLGMLAAIE VAVPGKVIET LSNPYGIATV FNLSPEETKN IVPMARALIG
NRSAVVVKTP SGDVKARAIP AGNLELLAQG RSVRVDVAAG AEAIMKAVDG CGRLDNVTGE
SGTNIGGMLE HVRQTMAELT NKPSSEIFIQ DLLAVDTSVP VSVTGGLAGE FSLEQAVGIA
SMVKSDRLQM AMIAREIEQK LNIDVQIGGA EAEAAILGAL TTPGTTRPLA ILDLGAGSTD
ASIINPKGDI IATHLAGAGD MVTMIIAREL GLEDRYLAEE IKKYPLAKVE SLFHLRHEDG
SVQFFSTPLP PAVFARVCVV KADELVPLPG DLALEKVRAI RRSAKERVFV TNALRALRQV
SPTGNIRDIP FVVLVGGSSL DFEVPQLVTD ALAHYRLVAG RGNIRGSEGP RNAVATGLIL
SWHKEFAHER
