5M6D

Streptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (SpGAPDH) crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Deciphering Key Residues Involved in the Virulence-promoting Interactions between Streptococcus pneumoniae and Human Plasminogen.

Moreau, C.Terrasse, R.Thielens, N.M.Vernet, T.Gaboriaud, C.Di Guilmi, A.M.

(2017) J Biol Chem 292: 2217-2225

  • DOI: 10.1074/jbc.M116.764209
  • Primary Citation of Related Structures:  
    5M6D

  • PubMed Abstract: 
  • Bacterial pathogens recruit circulating proteins to their own surfaces, co-opting the host protein functions as a mechanism of virulence. Particular attention has focused on the binding of plasminogen (Plg) to bacterial surfaces, as it has been shown ...

    Bacterial pathogens recruit circulating proteins to their own surfaces, co-opting the host protein functions as a mechanism of virulence. Particular attention has focused on the binding of plasminogen (Plg) to bacterial surfaces, as it has been shown that this interaction contributes to bacterial adhesion to host cells, invasion of host tissues, and evasion of the immune system. Several bacterial proteins are known to serve as receptors for Plg including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a cytoplasmic enzyme that appears on the cell surface in this moonlighting role. Although Plg typically binds to these receptors via several lysine-binding domains, the specific interactions that occur have not been documented in all cases. However, identification of the relevant residues could help define strategies for mitigating the virulence of important human pathogens, such as Streptococcus pneumoniae (Sp). To shed light on this question, we have described a combination of peptide-spot array screening, competition and SPR assays, high-resolution crystallography, and mutational analyses to characterize the interaction between SpGAPDH and Plg. We identified three SpGAPDH lysine residues that were instrumental in defining the kinetic and thermodynamic parameters of the interaction. Altogether, the integration of the data presented in this work allows us to propose a structural model for the molecular interaction of the SpGAPDH-Plg complex.


    Organizational Affiliation

    From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Commissariat à l'Energie Atomique (CEA), CNRS, 38044 Grenoble, France anne-marie.di-guilmi@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseAB355Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
gapdhgapgapAgapA_3ERS003549_02320ERS019166_02194ERS019420_02001ERS019499_02096ERS020135_02122ERS020141_02006ERS020142_02114ERS020143_02138ERS020145_02042ERS020146_02116ERS020147_02108ERS020151_01255ERS020155_02130ERS020157_02177ERS020178_05802ERS020520_01871ERS020522_01677ERS020523_02061ERS020524_02058ERS020526_04928ERS020526_06565ERS020527_02055ERS020531_01991ERS020539_02263ERS020541_02011ERS020726_03159ERS020822_04318ERS020831_02217ERS020873_02164ERS020881_02198ERS021047_02054ERS021354_07537ERS021360_02109ERS021447_07389ERS022199_02215ERS022232_07453ERS096208_02293ERS232497_02152ERS367628_02144ERS367811_01576ERS394170_00349ERS409165_02221ERS409372_02114ERS409444_01606ERS455085_02183ERS515225_02154SpnNT_02067A4260_06920AZJ28_04050AZJ96_07530AZK21_05520AZK39_10340ERS019258_02112ERS020087_02061ERS020524_02123ERS020598_02130ERS020948_01215ERS021280_02223ERS232443_02051ERS367973_02185ERS409062_02223GM528_10005GM530_10330GM532_03730GM533_10130GM537_10140GM538_10275GM539_10415GM541_10180GM542_10020GM548_10220NCTC12140_00362SAMEA104035127_00626SAMEA104035134_01371SAMEA104035170_01780SAMEA104035911_02058SAMEA104154639_02274SAMEA104154682_01206SAMEA2050326_02288SAMEA2052026_02314SAMEA2203388_02251SAMEA2203858_02221SAMEA2335963_01215SAMEA2335968_02058SAMEA2335976_00349SAMEA2696310_01609SAMEA2696394_02060SAMEA2796704_00374SAMEA2796719_02221SAMEA3172940_02100SAMEA3207004_02069SAMEA3207192_02187SAMEA3207204_02060SAMEA3232645_02306SAMEA3309693_02134SAMEA3309804_01851SAMEA3353184_01890SAMEA3353431_00915SAMEA3353590_02244SAMEA3353631_02382SAMEA3354309_02226SAMEA3354337_01606SAMEA3389217_00848SAMEA3389847_02311SAMEA3430861_01379SAMEA3447932_01735SAMEA3448014_00792SAMEA3714007_01961SAMEA3714180_02032SAMEA3714202_01356SAMEA3714270_02106SAMEA3714340_01937SAMEA3714392_01900SAMEA4388349_02337

EC: 1.2.1
Find proteins for I6L8L9 (Streptococcus pneumoniae)
Explore I6L8L9 
Go to UniProtKB:  I6L8L9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSU
Query on CSU
A,BL-PEPTIDE LINKINGC3 H7 N O5 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.041α = 90
b = 130.237β = 119.64
c = 79.837γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-02

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Advisory, Author supporting evidence
  • Version 1.3: 2018-01-31
    Changes: Database references
  • Version 1.4: 2019-10-16
    Changes: Data collection