5YRV

Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.

Shibata, N.Sueyoshi, Y.Higuchi, Y.Toraya, T.

(2018) Angew Chem Int Ed Engl 57: 7830-7835

  • DOI: 10.1002/anie.201803591
  • Primary Citation of Related Structures:  
    5YRT, 5YRV, 5YSH, 5YSN, 5YSR

  • PubMed Abstract: 
  • The crystal structures of the B 12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product ...

    The crystal structures of the B 12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diol dehydrase alpha subunitA, D, G, J554Klebsiella oxytocaMutation(s): 0 
Gene Names: pddApduCAB185_12495SAMEA2273575_05741AGF18_15670C2U42_33605C2U44_05475
EC: 4.2.1.28
UniProt
Find proteins for Q59470 (Klebsiella oxytoca)
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Go to UniProtKB:  Q59470
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Diol dehydrase beta subunitB, E, H, K200Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB
EC: 4.2.1.28
UniProt
Find proteins for Q59471 (Klebsiella oxytoca)
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Go to UniProtKB:  Q59471
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Diol dehydrase gamma subunitC, F, I, L137Klebsiella oxytocaMutation(s): 0 
Gene Names: pddCpduEpduE_1AB185_12485SAMEA2273639_01293SAMEA2273697_01477C2U42_33595
EC: 4.2.1.28
UniProt
Find proteins for Q59472 (Klebsiella oxytoca)
Explore Q59472 
Go to UniProtKB:  Q59472
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
CA [auth E], LA [auth H], T [auth B], TA [auth K]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
5AD (Subject of Investigation/LOI)
Query on 5AD

Download Ideal Coordinates CCD File 
IA [auth G], Q [auth A], QA [auth J], Z [auth D]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
HA [auth G], P [auth A], Y [auth D]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth G], M [auth A], NA [auth J], V [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
FA [auth G], GA [auth G], N [auth A], O [auth A], OA [auth J], PA [auth J], W [auth D], X [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , DA [auth F] , JA [auth G] , KA [auth G] , MA [auth I] , R [auth A] , RA [auth J] , 
AA [auth D], BA [auth D], DA [auth F], JA [auth G], KA [auth G], MA [auth I], R [auth A], RA [auth J], S [auth A], SA [auth J], U [auth C], UA [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.777α = 80.61
b = 95.666β = 87.77
c = 114.514γ = 81.25
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2017-11-10 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Shibata, N.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release