ID Q59471_KLEOX Unreviewed; 224 AA.
AC Q59471;
DT 01-NOV-1996, integrated into UniProtKB/TrEMBL.
DT 01-NOV-1996, sequence version 1.
DT 27-MAR-2024, entry version 122.
DE SubName: Full=Diol dehydrase beta subunit {ECO:0000313|EMBL:BAA08100.1};
DE EC=4.2.1.28 {ECO:0000313|EMBL:BAA08100.1};
GN Name=pddB {ECO:0000313|EMBL:BAA08100.1};
OS Klebsiella oxytoca.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX NCBI_TaxID=571 {ECO:0000313|EMBL:BAA08100.1};
RN [1] {ECO:0000313|EMBL:BAA08100.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 8724 {ECO:0000313|EMBL:BAA08100.1};
RX PubMed=7706251; DOI=10.1074/jbc.270.13.7142;
RA Tobimatsu T., Hara T., Sakaguchi M., Kishimoto Y., Wada Y., Isoda M.,
RA Sakai T., Toraya T.;
RT "Molecular cloning, sequencing, and expression of the genes encoding
RT adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca.";
RL J. Biol. Chem. 270:7142-7148(1995).
RN [2] {ECO:0007829|PDB:1DIO}
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH COB(II)ALAMIN.
RX PubMed=10467140; DOI=10.1016/s0969-2126(99)80126-9;
RA Shibata N., Masuda J., Tobimatsu T., Toraya T., Suto K., Morimoto Y.,
RA Yasuoka N.;
RT "A new mode of B12 binding and the direct participation of a potassium ion
RT in enzyme catalysis: X-ray structure of diol dehydratase.";
RL Structure 7:997-1008(1999).
RN [3] {ECO:0007829|PDB:1EEX, ECO:0007829|PDB:1EGM}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH CYANOCOB(III)ALAMIN.
RX PubMed=10903944; DOI=10.1016/s0969-2126(00)00164-7;
RA Masuda J., Shibata N., Morimoto Y., Toraya T., Yasuoka N.;
RT "How a protein generates a catalytic radical from coenzyme B(12): X-ray
RT structure of a diol-dehydratase-adeninylpentylcobalamin complex.";
RL Structure 8:775-788(2000).
RN [4] {ECO:0007829|PDB:1IWB}
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH COB(II)ALAMIN.
RX PubMed=12379103; DOI=10.1021/bi026104z;
RA Shibata N., Masuda J., Morimoto Y., Yasuoka N., Toraya T.;
RT "Substrate-induced conformational change of a coenzyme B12-dependent
RT enzyme: crystal structure of the substrate-free form of diol dehydratase.";
RL Biochemistry 41:12607-12617(2002).
RN [5] {ECO:0007829|PDB:1UC4, ECO:0007829|PDB:1UC5}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CYANOCOB(III)ALAMIN.
RX PubMed=12684496; DOI=10.1074/jbc.m301513200;
RA Shibata N., Nakanishi Y., Fukuoka M., Yamanishi M., Yasuoka N., Toraya T.;
RT "Structural rationalization for the lack of stereospecificity in coenzyme
RT B12-dependent diol dehydratase.";
RL J. Biol. Chem. 278:22717-22725(2003).
RN [6] {ECO:0007829|PDB:3AUJ}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH CA(2+).
RX PubMed=22221669; DOI=10.1111/j.1742-4658.2012.08470.x;
RA Yamanishi M., Kinoshita K., Fukuoka M., Saito T., Tanokuchi A., Ikeda Y.,
RA Obayashi H., Mori K., Shibata N., Tobimatsu T., Toraya T.;
RT "Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to
RT the mechanism-based inactivation by glycerol and act on longer chain 1,2-
RT diols.";
RL FEBS J. 279:793-804(2012).
RN [7] {ECO:0007829|PDB:5YRT, ECO:0007829|PDB:5YRV}
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 46-224 IN COMPLEX WITH
RP COB(II)ALAMIN.
RX PubMed=29797764; DOI=10.1002/anie.201803591;
RA Shibata N., Sueyoshi Y., Higuchi Y., Toraya T.;
RT "Direct Participation of a Peripheral Side Chain of a Corrin Ring in
RT CoenzymeB12 Catalysis.";
RL Angew. Chem. Int. Ed. 57:7830-7835(2018).
RN [8] {ECO:0007829|PDB:7XRK, ECO:0007829|PDB:7XRL}
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 46-224 IN COMPLEX WITH
RP COB(II)ALAMIN.
RX PubMed=35974426; DOI=10.1002/chem.202202196;
RA Shibata N., Higuchi Y., Krautler B., Toraya T.;
RT "Structural Insights into the Very Low Activity of the Homocoenzyme
RT B12 Adenosylmethylcobalamin in Coenzyme B12
RT -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.";
RL Chemistry 28:e202202196-e202202196(2022).
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DR EMBL; D45071; BAA08100.1; -; Genomic_DNA.
DR PIR; B56111; B56111.
DR PDB; 1DIO; X-ray; 2.20 A; B/E=1-224.
DR PDB; 1EEX; X-ray; 1.70 A; B/E=1-224.
DR PDB; 1EGM; X-ray; 1.85 A; B/E=1-224.
DR PDB; 1EGV; X-ray; 1.75 A; B/E=1-224.
DR PDB; 1IWB; X-ray; 1.85 A; B/E=1-224.
DR PDB; 1UC4; X-ray; 1.80 A; B/E=1-224.
DR PDB; 1UC5; X-ray; 2.30 A; B/E=1-224.
DR PDB; 3AUJ; X-ray; 2.10 A; B/E=1-224.
DR PDB; 5YRT; X-ray; 1.70 A; B/E/H/K=46-224.
DR PDB; 5YRV; X-ray; 1.55 A; B/E/H/K=46-224.
DR PDB; 5YSH; X-ray; 1.90 A; B/E/H/K=46-224.
DR PDB; 7XRK; X-ray; 2.30 A; B/E=46-224.
DR PDB; 7XRL; X-ray; 1.75 A; B/E=46-224.
DR PDBsum; 1DIO; -.
DR PDBsum; 1EEX; -.
DR PDBsum; 1EGM; -.
DR PDBsum; 1EGV; -.
DR PDBsum; 1IWB; -.
DR PDBsum; 1UC4; -.
DR PDBsum; 1UC5; -.
DR PDBsum; 3AUJ; -.
DR PDBsum; 5YRT; -.
DR PDBsum; 5YRV; -.
DR PDBsum; 5YSH; -.
DR AlphaFoldDB; Q59471; -.
DR SMR; Q59471; -.
DR IntAct; Q59471; 2.
DR MINT; Q59471; -.
DR BRENDA; 4.2.1.28; 2811.
DR EvolutionaryTrace; Q59471; -.
DR GO; GO:0050215; F:propanediol dehydratase activity; IEA:UniProtKB-EC.
DR DisProt; DP01028; -.
DR Gene3D; 3.40.50.10150; B12-dependent dehydatase associated subunit; 1.
DR InterPro; IPR010254; B12-dep_deHydtase_bsu.
DR InterPro; IPR003208; Dehydtase/Dehydtase_re.
DR InterPro; IPR025541; Ppandiol/glycerol_DHydtase_msu.
DR Pfam; PF02288; Dehydratase_MU; 1.
DR PIRSF; PIRSF018506; Prpndl_dhdrts_md; 1.
DR SUPFAM; SSF52968; B12-dependent dehydatase associated subunit; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1EEX};
KW Lyase {ECO:0000313|EMBL:BAA08100.1}.
FT BINDING 112
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 112
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 135
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /ligand_note="covalent"
FT /evidence="ECO:0007829|PDB:7XRL"
FT BINDING 135
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 137
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 137
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 150
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 150
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 155
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 155
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 156
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 156
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 157
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 157
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
FT BINDING 197
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:7XRK, ECO:0007829|PDB:7XRL"
FT BINDING 200
FT /ligand="cob(II)alamin"
FT /ligand_id="ChEBI:CHEBI:16304"
FT /evidence="ECO:0007829|PDB:1DIO, ECO:0007829|PDB:1IWB"
FT BINDING 200
FT /ligand="cyanocob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:17439"
FT /evidence="ECO:0007829|PDB:1EGM, ECO:0007829|PDB:1UC4"
SQ SEQUENCE 224 AA; 24114 MW; C0A7C45A55CFAC7D CRC64;
MEINEKLLRQ IIEDVLSEMK GSDKPVSFNA PAASAAPQAT PPAGDGFLTE VGEARQGTQQ
DEVIIAVGPA FGLAQTVNIV GIPHKSILRE VIAGIEEEGI KARVIRCFKS SDVAFVAVEG
NRLSGSGISI GIQSKGTTVI HQQGLPPLSN LELFPQAPLL TLETYRQIGK NAARYAKRES
PQPVPTLNDQ MARPKYQAKS AILHIKETKY VVTGKNPQEL RVAL
//