› 1iwp

X-ray diffraction
2.1Å resolution

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

Released:
DOI: 10.2210/pdb1iwp/pdb
PDB entry 1iwp coloured by chain, front view.
PDB entry 1iwp coloured by chain, side view.
PDB entry 1iwp coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
Yamanishi M, Yunoki M, Tobimatsu T, Sato H, Matsui J, Dokiya A, Iuchi Y, Oe K, Suto K, Shibata N, Morimoto Y, Yasuoka N, Toraya T
Eur J Biochem 269 4484-94 (2002)
PMID: 12230560

Function and Biology Details

Reactions catalysed: 
Glycerol = 3-hydroxypropanal + H(2)O
Propane-1,2-diol = propanal + H(2)O
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-126622 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Diol/glycerol dehydratase large subunit domain-containing protein Chains: A, L
Molecule details ›
Chains: A, L
Length: 555 amino acids
Theoretical weight: 60.71 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59476 (Residues: 1-555; Coverage: 100%)
Gene names: AI2879V1_4568, APT76_15605, B5L96_24300, B6I68_11220, BANRA_00607, BANRA_00639, BL124_00019860, BVZ24_13660, DM078_01095, DM087_03040, DMR11_11685, DW281_27630, EAO17_10385, FCH06_007315, FNZ01_09005, FXN67_07665, G4V31_24485, GJJ08_003260, GJJ18_07115, GJJ21_12385, GNF00_15835, HV207_03110, NCTC13635_02952, NCTC204_02861, NCTC8849_05452, NCTC9140_07207, NCTC9637_01198, QIG75_16700, SAMEA2273811_02280, SAMEA3499874_03316, SAMEA3499901_03621, SAMEA3512100_03933, SAMEA3515122_03388, SAMEA3531867_02862, SAMEA3538424_01943, SAMEA3538658_02030, SAMEA3538828_04665, SAMEA3649591_00069, SAMEA3649615_02814, SAMEA3649733_03822, SAMEA3727706_00617, SAMEA4364603_00761, SAMEA4370542_01951, SAMEA4873597_01695, SAMEA4873632_04144, VKR_00647, dhaB, dhaB1, gldA, pduC
Sequence domains: Dehydratase large subunit
Structure domains: Diol/glycerol dehydratase, large subunit
Propanediol/glycerol family dehydratase medium subunit Chains: B, E
Molecule details ›
Chains: B, E
Length: 194 amino acids
Theoretical weight: 21.39 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: O08505 (Residues: 1-194; Coverage: 100%)
Gene names: FXN67_07660, IE995_10825, NCTC11679_00707, SAMEA2273811_02279, VKR_00648, gldB, pduD_1, pduD_2
Sequence domains: Dehydratase medium subunit
Structure domains: B12-dependent dehydatase associated subunit
Glycerol dehydratase Chains: G, M
Molecule details ›
Chains: G, M
Length: 141 amino acids
Theoretical weight: 16.13 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59475 (Residues: 1-141; Coverage: 100%)
Gene names: AI2879V1_4570, APT76_15595, B5L96_24290, B6I68_11230, BANRA_00609, BANRA_00641, BL124_00019850, BVZ24_13670, DM078_01105, DM087_03030, DMR11_11675, EAO17_10375, FCH06_007305, FNZ01_09015, FXN67_07655, G4V31_24475, GJD55_14745, GJJ08_003270, GJJ13_003135, GJJ18_07105, GJJ21_12375, HV207_03120, NCTC11679_00708, NCTC13443_06523, NCTC13465_03592, NCTC204_02863, NCTC8849_05450, NCTC9140_07205, NCTC9637_01200, QIG75_16710, SAMEA2273811_02278, SAMEA3499874_03318, SAMEA3499901_03623, SAMEA3512100_03935, SAMEA3531867_02860, SAMEA3538424_01945, SAMEA3538658_02032, SAMEA3538828_04667, SAMEA3649591_00071, SAMEA3649733_03820, SAMEA3727706_00615, SAMEA4364603_00763, SAMEA4873597_01697, SAMEA4873632_04142, VKR_00649, dhaB3, dhaE, gldC, pduE, pduE_1, pduE_2, pduE_3
Sequence domains: Dehydratase small subunit
Structure domains: Propanediol/glycerol dehydratase, small subunit

Ligands and Environments


Cofactor: Ligand B12 2 x B12
2 bound ligands:
Ligand K 2 x K
Ligand PGO 2 x PGO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL40B2
Spacegroup: P21
Unit cell:
a: 81.38Å b: 108.223Å c: 113.141Å
α: 90° β: 96.75° γ: 90°
R-values:
R R work R free
0.209 0.209 0.247
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Metabolic engineering for the microbial production of 1,3-propanediol.
Nakamura et al. (2003)
15 more

7 mentions without citation

Computational enzyme design approaches with significant biological outcomes: progress and challenges.
Li et al. (2012)
6 more