1XRS

Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.

Berkovitch, F.Behshad, E.Tang, K.H.Enns, E.A.Frey, P.A.Drennan, C.L.

(2004) Proc Natl Acad Sci U S A 101: 15870-15875

  • DOI: 10.1073/pnas.0407074101
  • Primary Citation of Related Structures:  
    1XRS

  • PubMed Abstract: 
  • Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form o ...

    Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-lysine 5,6-aminomutase alpha subunitA516Acetoanaerobium sticklandiiMutation(s): 0 
Gene Names: KamDE
EC: 5.4.3.3
Find proteins for E3PRJ5 (Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654))
Explore E3PRJ5 
Go to UniProtKB:  E3PRJ5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D-lysine 5,6-aminomutase beta subunitB262Acetoanaerobium sticklandiiMutation(s): 0 
Gene Names: KamDE
EC: 5.4.3.3
Find proteins for E3PRJ4 (Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654))
Explore E3PRJ4 
Go to UniProtKB:  E3PRJ4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download CCD File 
B
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
5AD
Query on 5AD

Download CCD File 
B
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.7α = 90
b = 99.7β = 90
c = 168.8γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-10-24
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description