5EOM

Structure of full-length human MAB21L1 with bound CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Literature

Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1.

de Oliveira Mann, C.C.Kiefersauer, R.Witte, G.Hopfner, K.P.

(2016) Sci Rep 6: 27498-27498

  • DOI: https://doi.org/10.1038/srep27498
  • Primary Citation of Related Structures:  
    5EOG, 5EOM

  • PubMed Abstract: 

    The exceptionally conserved metazoan MAB21 proteins are implicated in cell fate decisions and share considerable sequence homology with the cyclic GMP-AMP synthase. cGAS is the major innate immune sensor for cytosolic DNA and produces the second messenger 2'-5', 3'-5' cyclic GMP-AMP. Little is known about the structure and biochemical function of other proteins of the cGAS-MAB21 subfamily, such as MAB21L1, MAB21L2 and MAB21L3. We have determined the crystal structure of human full-length MAB21L1. Our analysis reveals high structural conservation between MAB21L1 and cGAS but also uncovers important differences. Although monomeric in solution, MAB21L1 forms a highly symmetric double-pentameric oligomer in the crystal, raising the possibility that oligomerization could be a feature of MAB21L1. In the crystal, MAB21L1 is in an inactive conformation requiring a conformational change - similar to cGAS - to develop any nucleotidyltransferase activity. Co-crystallization with NTP identified a putative ligand binding site of MAB21 proteins that corresponds to the DNA binding site of cGAS. Finally, we offer a structure-based explanation for the effects of MAB21L2 mutations in patients with eye malformations. The underlying residues participate in fold-stabilizing interaction networks and mutations destabilize the protein. In summary, we provide a first structural framework for MAB21 proteins.


  • Organizational Affiliation

    Ludwig-Maximilians-Universität München, Gene Center and Dept. of Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mab-21-like 1362Homo sapiensMutation(s): 0 
Gene Names: MAB21L1CAGR1Nbla00126
UniProt & NIH Common Fund Data Resources
Find proteins for Q13394 (Homo sapiens)
Explore Q13394 
Go to UniProtKB:  Q13394
PHAROS:  Q13394
GTEx:  ENSG00000180660 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13394
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTP
Query on CTP

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
DA [auth J]
HA [auth C]
M [auth A]
AA [auth H],
CA [auth I],
DA [auth J],
HA [auth C],
M [auth A],
O [auth B],
Q [auth D],
S [auth E],
V [auth F],
X [auth G]
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
BA [auth I]
EA [auth C]
K [auth A]
N [auth B]
P [auth D]
BA [auth I],
EA [auth C],
K [auth A],
N [auth B],
P [auth D],
R [auth E],
T [auth F],
W [auth G],
Y [auth H],
Z [auth H]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
TMO
Query on TMO

Download Ideal Coordinates CCD File 
FA [auth C],
GA [auth C],
L [auth A],
U [auth F]
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115α = 90
b = 177.76β = 97.58
c = 134.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyGRK1721

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references