5NX9

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL) in complex with its products AMP and fumarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.

Van Laer, B.Kapp, U.Soler-Lopez, M.Moczulska, K.Paabo, S.Leonard, G.Mueller-Dieckmann, C.

(2018) Sci Rep 8: 18008-18008

  • DOI: 10.1038/s41598-018-36195-5
  • Primary Citation of Related Structures:  
    5NX8, 5NX9, 5NXA

  • PubMed Abstract: 
  • The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level ...

    The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.


    Organizational Affiliation

    Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France. christoph.mueller_dieckmann@esrf.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylosuccinate lyaseA, B, C, D487Homo sapiens neanderthalensisMutation(s): 0 
Gene Names: ADSLAMPS
EC: 4.3.2.2
UniProt
Find proteins for A0A384E0N4 (Homo sapiens neanderthalensis)
Explore A0A384E0N4 
Go to UniProtKB:  A0A384E0N4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SA (Subject of Investigation/LOI)
Query on 2SA

Download Ideal Coordinates CCD File 
O [auth B], Q [auth C]2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID
C14 H18 N5 O11 P
OFBHPPMPBOJXRT-VWJPMABRSA-N
 Ligand Interaction
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A], Z [auth D]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
FUM
Query on FUM

Download Ideal Coordinates CCD File 
AA [auth D], H [auth A]FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , DA [auth D] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , 
BA [auth D],  CA [auth D],  DA [auth D],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  P [auth B],  T [auth C],  U [auth C],  V [auth C],  X [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
W [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], N [auth B], R [auth C], S [auth C], Y [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 107.49β = 90
c = 209.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references