7VYJ

The structure of GdmN in complex with carbamoyl adenylate intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies.

Wei, J.Zhang, X.Zhou, Y.Cheng, X.Lin, Z.Tang, M.Zheng, J.Wang, B.Kang, Q.Bai, L.

(2022) Nat Commun 13: 6617-6617

  • DOI: https://doi.org/10.1038/s41467-022-34387-2
  • Primary Citation of Related Structures:  
    7VX0, 7VYJ, 7VYO, 7VYP, 7VZN, 7VZQ, 7VZU, 7VZY, 7VZZ

  • PubMed Abstract: 

    Iterative enzymes, which catalyze sequential reactions, have the potential to improve the atom economy and diversity of industrial enzymatic processes. Redesigning one-step enzymes to be iterative biocatalysts could further enhance these processes. Carbamoyltransferases (CTases) catalyze carbamoylation, an important modification for the bioactivity of many secondary metabolites with pharmaceutical applications. To generate an iterative CTase, we determine the X-ray structure of GdmN, a one-step CTase involved in ansamycin biosynthesis. GdmN forms a face-to-face homodimer through unusual C-terminal domains, a previously unknown functional form for CTases. Structural determination of GdmN complexed with multiple intermediates elucidates the carbamoylation process and identifies key binding residues within a spacious substrate-binding pocket. Further structural and computational analyses enable multi-site enzyme engineering, resulting in an iterative CTase with the capacity for successive 7-O and 3-O carbamoylations. Our findings reveal a subclade of the CTase family and exemplify the potential of protein engineering for generating iterative enzymes.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GdmN
A, B
682Streptomyces hygroscopicusMutation(s): 0 
Gene Names: gdmN
UniProt
Find proteins for Q84G19 (Streptomyces hygroscopicus)
Explore Q84G19 
Go to UniProtKB:  Q84G19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84G19
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA0 (Subject of Investigation/LOI)
Query on CA0

Download Ideal Coordinates CCD File 
D [auth A],
U [auth B]
5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine
C11 H15 N6 O8 P
CHSNPOFVFYPELH-KQYNXXCUSA-N
CP
Query on CP

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DA [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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E [auth A],
F [auth A],
V [auth B],
W [auth B],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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R [auth A],
S [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
H [auth A]
I [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
T [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.531α = 90
b = 110.531β = 90
c = 231.46γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government2019YFA0905400
Other government2021YFC2100600
Other government31830104
Other government31800023
Other government31801036
Other governmentU1703236
Other government17JC1403600

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description