4ML7

Crystal structure of Brucella abortus PliC in complex with human lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Inhibition of Human Lysozyme by PliC from Brucella abortus

Um, S.H.Kim, J.S.Kim, K.Kim, N.Cho, H.S.Ha, N.C.

(2013) Biochemistry 52: 9385-9393

  • DOI: 10.1021/bi401241c
  • Primary Citation of Related Structures:  
    4MIR, 4MIS, 4ML7

  • PubMed Abstract: 
  • Lysozymes are the first line of defense for a diverse range of organisms that catalyze the degradation of bacterial peptidoglycan. Gram-negative bacteria produce proteinaceous lysozyme inhibitors to protect themselves from the action of lysozymes. To date, MliC or PliC (membrane-bound or periplasmic inhibitor of c-type lysozyme, respectively) has been found in various Gram-negative bacteria ...

    Lysozymes are the first line of defense for a diverse range of organisms that catalyze the degradation of bacterial peptidoglycan. Gram-negative bacteria produce proteinaceous lysozyme inhibitors to protect themselves from the action of lysozymes. To date, MliC or PliC (membrane-bound or periplasmic inhibitor of c-type lysozyme, respectively) has been found in various Gram-negative bacteria. Here, we report the crystal structures of Brucella abortus PliC and its complex with human c-type lysozyme. The complex structure demonstrates that the invariant loop of MliC/PliC plays a crucial role in the inhibition of lysozyme via its insertion into the active site cleft of the lysozyme, as previously observed in the complex structure of Pseudomonas aeruginosa MliC and chicken c-type lysozyme. We identified a new binding interface between a loop adjacent to the active site of human lysozyme and a loop carrying Glu112 of B. abortus PliC, the structure of which was disordered in P. aeruginosa MliC. Because MliC/PliC family members have been implicated as putative colonization or virulence factors, the structures and mechanism of action of MliC/PliC will be relevant to the control of bacterial growth in animal hosts.


    Organizational Affiliation

    College of Pharmacy and Research Institute for Drug Development, Pusan National University , Busan 609-735, Republic of Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA, C130Homo sapiensMutation(s): 0 
Gene Names: LYZLZM
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens)
Explore P61626 
Go to UniProtKB:  P61626
PHAROS:  P61626
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HumanlysozymeB, D99Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.253α = 90
b = 88.984β = 90
c = 66.206γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Source and taxonomy