crystal structure of human MMACHC

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history


Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function.

Froese, D.S.Krojer, T.Wu, X.Shrestha, R.Kiyani, W.von Delft, F.Gravel, R.A.Oppermann, U.Yue, W.W.

(2012) Biochemistry 51: 5083-5090

  • DOI: https://doi.org/10.1021/bi300150y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Defects in the MMACHC gene represent the most common disorder of cobalamin (Cbl) metabolism, affecting synthesis of the enzyme cofactors adenosyl-Cbl and methyl-Cbl. The encoded MMACHC protein binds intracellular Cbl derivatives with different upper axial ligands and exhibits flavin mononucleotide (FMN)-dependent decyanase activity toward cyano-Cbl as well as glutathione (GSH)-dependent dealkylase activity toward alkyl-Cbls. We determined the structure of human MMACHC·adenosyl-Cbl complex, revealing a tailor-made nitroreductase scaffold which binds adenosyl-Cbl in a "base-off, five-coordinate" configuration for catalysis. We further identified an arginine-rich pocket close to the Cbl binding site responsible for GSH binding and dealkylation activity. Mutation of these highly conserved arginines, including a replication of the prevalent MMACHC missense mutation, Arg161Gln, disrupts GSH binding and dealkylation. We further showed that two Cbl-binding monomers dimerize to mediate the reciprocal exchange of a conserved "PNRRP" loop from both subunits, serving as a protein cap for the upper axial ligand in trans and required for proper dealkylation activity. Our dimeric structure is supported by solution studies, where dimerization is triggered upon binding its substrate adenosyl-Cbl or cofactor FMN. Together our data provide a structural framework to understanding catalytic function and disease mechanism for this multifunctional enzyme.

  • Organizational Affiliation

    Structural Genomics Consortium, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylmalonic aciduria and homocystinuria type C protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
286Homo sapiensMutation(s): 0 
Gene Names: MMACHC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4U1 (Homo sapiens)
Explore Q9Y4U1 
Go to UniProtKB:  Q9Y4U1
GTEx:  ENSG00000132763 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4U1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B12

Download Ideal Coordinates CCD File 
AC [auth P]
CA [auth D]
CB [auth J]
FA [auth E]
FB [auth K]
AC [auth P],
CA [auth D],
CB [auth J],
FA [auth E],
FB [auth K],
KA [auth F],
KB [auth L],
NA [auth G],
NB [auth M],
Q [auth A],
SB [auth N],
TA [auth H],
V [auth B],
VB [auth O],
WA [auth I],
X [auth C]
C62 H89 Co N13 O14 P
Query on 5AD

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth I]
BA [auth D]
BB [auth J]
HA [auth E]
AA [auth C],
AB [auth I],
BA [auth D],
BB [auth J],
HA [auth E],
IB [auth K],
JA [auth F],
JB [auth L],
QA [auth G],
QB [auth M],
RA [auth G],
RB [auth N],
SA [auth H],
T [auth A],
U [auth B],
YB [auth O],
ZA [auth I],
ZB [auth P]
C10 H13 N5 O3
Query on FLC

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BC [auth P]
DA [auth D]
DB [auth J]
GA [auth E]
GB [auth K]
BC [auth P],
DA [auth D],
DB [auth J],
GA [auth E],
GB [auth K],
LA [auth F],
LB [auth L],
OA [auth G],
OB [auth M],
R [auth A],
TB [auth N],
UA [auth H],
W [auth B],
WB [auth O],
XA [auth I],
Y [auth C]
C6 H5 O7
Query on DHL

Download Ideal Coordinates CCD File 
CC [auth P]
EA [auth D]
EB [auth J]
HB [auth K]
MA [auth F]
CC [auth P],
EA [auth D],
EB [auth J],
HB [auth K],
MA [auth F],
MB [auth L],
PA [auth G],
PB [auth M],
S [auth A],
UB [auth N],
VA [auth H],
XB [auth O],
YA [auth I],
Z [auth C]
C2 H7 N S
Query on EDO

Download Ideal Coordinates CCD File 
DC [auth P],
EC [auth P],
IA [auth E]
C2 H6 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.664α = 88.53
b = 71.96β = 85.25
c = 300.055γ = 83.76
Software Package:
Software NamePurpose
GDAdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Non-polymer description
  • Version 1.2: 2015-04-15
    Changes: Database references