3H9Q

Crystal structure of E. coli MccB + SeMet MccA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.

Regni, C.A.Roush, R.F.Miller, D.J.Nourse, A.Walsh, C.T.Schulman, B.A.

(2009) EMBO J 28: 1953-1964

  • DOI: 10.1038/emboj.2009.146
  • Primary Citation of Related Structures:  
    3H5R, 3H5N, 3H5A, 3H9Q, 3H9G, 3H9J

  • PubMed Abstract: 
  • The 39-kDa Escherichia coli enzyme MccB catalyses a remarkable posttranslational modification of the MccA heptapeptide during the biosynthesis of microcin C7 (MccC7), a 'Trojan horse' antibiotic. The approximately 260-residue C-terminal region of Mcc ...

    The 39-kDa Escherichia coli enzyme MccB catalyses a remarkable posttranslational modification of the MccA heptapeptide during the biosynthesis of microcin C7 (MccC7), a 'Trojan horse' antibiotic. The approximately 260-residue C-terminal region of MccB is homologous to ubiquitin-like protein (UBL) activating enzyme (E1) adenylation domains. Accordingly, MccB-catalysed C-terminal MccA-acyl-adenylation is reminiscent of the E1-catalysed activation reaction. However, unlike E1 substrates, which are UBLs with a C-terminal di-glycine sequence, MccB's substrate, MccA, is a short peptide with an essential C-terminal Asn. Furthermore, after an intramolecular rearrangement of MccA-acyl-adenylate, MccB catalyses a second, unique reaction, producing a stable phosphoramidate-linked analogue of acyl-adenylated aspartic acid. We report six-crystal structures of MccB in apo, substrate-, intermediate-, and inhibitor-bound forms. Structural and kinetic analyses reveal a novel-peptide clamping mechanism for MccB binding to heptapeptide substrates and a dynamic-active site for catalysing dual adenosine triphosphate-consuming reactions. The results provide insight into how a distinctive member of the E1 superfamily carries out two-step activation for generating the peptidyl-antibiotic MccC7.


    Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MccB proteinABCD353Escherichia coliMutation(s): 0 
Gene Names: mccB
Find proteins for Q47506 (Escherichia coli)
Explore Q47506 
Go to UniProtKB:  Q47506
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Microcin C7 ANALOGEFGH7Escherichia coliMutation(s): 0 
Gene Names: mccA
Find proteins for Q47505 (Escherichia coli)
Explore Q47505 
Go to UniProtKB:  Q47505
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
E,F,G,HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001126
Query on PRD_001126
E, F, G, HSelenomethionine derivative of Microcin C7Polypeptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 138.597β = 92.06
c = 81.375γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Non-polymer description, Structure summary
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-07-03
    Changes: Other
  • Version 1.5: 2017-11-01
    Changes: Advisory, Refinement description