5OED

Human Rab32:GDP in complex with Salmonella GtgE C45A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The protease GtgE from Salmonella exclusively targets inactive Rab GTPases.

Wachtel, R.Brauning, B.Mader, S.L.Ecker, F.Kaila, V.R.I.Groll, M.Itzen, A.

(2018) Nat Commun 9: 44-44

  • DOI: 10.1038/s41467-017-02110-1
  • Primary Citation of Related Structures:  
    5OED, 5OEC

  • PubMed Abstract: 
  • Salmonella infections require the delivery of bacterial effectors into the host cell that alter the regulation of host defense mechanisms. The secreted cysteine protease GtgE from S. Typhimurium manipulates vesicular trafficking by modifying the Rab32 subfamily via cleaving the regulatory switch I region ...

    Salmonella infections require the delivery of bacterial effectors into the host cell that alter the regulation of host defense mechanisms. The secreted cysteine protease GtgE from S. Typhimurium manipulates vesicular trafficking by modifying the Rab32 subfamily via cleaving the regulatory switch I region. Here we present a comprehensive biochemical, structural, and computational characterization of GtgE in complex with Rab32. Interestingly, GtgE solely processes the inactive GDP-bound GTPase. The crystal structure of the Rab32:GDP substrate in complex with the inactive mutant GtgE C45A reveals the molecular basis of substrate recognition. In combination with atomistic molecular dynamics simulations, the structural determinants for protein and activity-state specificity are identified. Mutations in a central interaction hub lead to loss of the strict GDP specificity. Our findings shed light on the sequence of host cell manipulation events during Salmonella infection and provide an explanation for the dependence on the co-secreted GTPase activating protein SopD2.


    Organizational Affiliation

    Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany. aymelt.itzen@tum.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GtgEA230Salmonella entericaMutation(s): 1 
Gene Names: 
gtgEIN36_21720IN69_16745IN77_18825A2H16_07055A3831_05295A6844_09675A6870_19920A6898_00535A7D45_11990A7F95_22390A9V16_06060AAT47_19635ABH29_02250AKH36_00070AL463_22290AMK51_05570AQ523_17220ASR56_00715AST35_06675AUD13_14280AWU43_00110AZF90_21570B5A57_07355B6K00_00075BCZ10_11695BH399_11345BSX00_00425BU284_04035BU700_15870C0X38_14625C0X54_05430C2763_23195C6254_22020C6269_18865CAR37_07980CBJ97_24585CBS00_03710CBS62_04370CDM42_00520CE314_04190CGY76_14880CID34_10830CID45_00350CIY18_21035CJ353_06675CJF95_06680CJT17_12980CK009_14340CKU74_12635CLK14_06970CMS46_20460COG57_04470COQ67_23070COQ74_20980CPK13_00505CQT16_04195CQW68_16290CRR30_05380CS198_04460CSK90_09180CTB03_20650CV257_14525CVX89_10495CX762_07010D0C46_17970D1275_06105D1766_20135D2H15_10740D3K32_05425D3Q81_09245D5375_11075D5389_05610D5403_17265D5465_23445D5489_05580D5563_20215D5565_18090D5598_06980D5714_02855D5K09_12530D5K19_20710D5S36_05560D5S75_14045D5T25_02945D5T50_02240D5T53_14175D5T55_17270D5U49_15005D5U61_00040D5U63_04635D5U72_03705D5U75_05945D6093_13775D6518_14190D6942_05020D6948_18910D6949_06955D6969_10640D6975_06860D6E71_06980D6E86_13705D6F52_21335D6F91_13015D6G02_05730D6G24_10990D6G47_12215D6G76_10910D6G87_17140D6H24_16375D6H36_03625D6H45_06965D6H57_00155D6H85_00440D6H96_01415D6I35_11405D6I55_04350D6I58_19965D6J27_16750D6M94_05240D6N21_00115D6N69_24145D6N74_06475D6O04_20895D6O30_13300D6O65_06975D6Y46_13695D7A03_06150D7A14_06025D7A65_03600D7B44_06945D7B51_18840D7B53_13940D7B65_20010D7B66_04995D7B84_24305D7B88_00040D7C00_07245D7C05_17970D7C06_14620D7C56_21275D7C59_06945D7C85_16590D7C86_05560D7D22_13280D7D38_22800D7E22_00115D7E26_03755D7F01_18030D7F60_12390D7F69_03755D7G05_13430D7G25_24005D7G28_14935D7G35_06945D7G42_06600D7G43_06950D7J26_12255D7J34_14610D7K26_15215D7L19_16755D7M32_00105D7T04_19490D7T97_00520D7U23_23780D7U29_18200D7U60_10375D7U94_18515D7V56_25745D7W42_14250D7W46_15125D7W92_20320D8I57_09620D8M87_20220D8N11_14945D8N25_19365D8N30_07130D8N31_08620D8N36_06940D8N44_11880D8N46_15915D8N55_00040D8N76_05725D8O28_19555D8O41_15990D8O75_14795D8O94_23175D8P26_25220D8P27_06870D8P70_13530D8Q16_06940D8Q18_05020D8Q38_06950D8T28_03550D8T94_06280D8T97_21760D8U37_21600D8U80_20795D8U85_04315D8U96_23985D8V04_18180D8V52_16405D8V55_24240D8Z08_04725D9789_17900D9804_00155D9813_24635D9841_19045D9893_12600D9904_02790D9908_16130D9940_21465D9970_05790D9A73_14565D9B00_00045D9B25_13805D9B35_18550D9B53_21280D9B88_04330D9N38_06955D9R37_20135D9R54_19440D9R86_23925D9T47_05400D9T56_03200D9T70_14185D9U02_05435D9Z40_06915DB909_19005DFW51_12690DH03_16525DKH31_18410DKM56_19365DKM82_15835DKT79_17490DLA46_21330DLO05_21825DLO13_14830DLO43_00205DM524_13445DM771_17825DM912_02410DMB22_02050DMJ05_04350DMM59_08695DMT37_17410DMV54_07825DO307_25510DOK24_00540DON15_07250DPH90_17165DPH94_07410DS006_21535DSC90_00135DT233_16080DT651_08660DTD68_13820DTS56_08930DV658_05420DWE28_17815DXI96_18765DXJ54_09650DXO64_19190DXS05_04975DYI64_14090EA079_09155EA847_07990EA863_09665EA865_24075EA890_09640EA919_07195EA948_06845EA989_08535EAA70_16180EAA74_24610EAA91_02175EAB27_13465EAB61_18770EAB70_17790EAB95_00115EAC03_21250EAC08_20860EAC27_18490EAC50_15090EAC52_08870EAC62_18490EAC94_06260EAD37_13190EAD40_13150EAD57_24825EAD82_10935EAF83_20885EAJ73_02795EAN17_09025EAN28_14945EAP40_22710EAP86_04035EAT60_11405EAT73_18205EAT75_18245EAT82_15680EAU30_07235EAU46_14940EAU57_20255EAU58_16800EAU66_05460EAU70_00110EAV12_16510EAV49_14075EAV62_14375EAW74_09800EAW87_07235EAX36_20850EAX53_16160EAY08_23195EBF44_00050EBF61_19345EBG75_24915EBG93_14050EBH52_17305EBH57_20375EBH58_18480EBH67_19460EBH87_08285EBI58_14565EE502_24090EE513_16505EEQ36_17950EF388_15350EF401_23935EF592_06845EF628_13855EF956_01570EF958_10235EF970_16630EF991_24265EFE59_15450EFH71_15680EFH94_00115EFI62_05335EFI71_23195EFJ16_09265EFW83_15760EFX99_18965EFY29_14055EFY62_16805EFY85_18500EFZ06_00210EFZ60_06755EG001_06110EG014_05650EG019_07140EG056_18875EG064_16165EG093_13610EG118_20935EG164_19500EG229_21035EG454_14735EG502_10115EG595_15010EG620_19220EG623_19785EG625_21005EG636_12495EG641_22750EG650_06355EG692_02500EG717_17490EG762_15680EG763_15480EG764_00565EG767_13870EG909_22730EG952_16190EG958_16735EG959_21010EG974_05770EGA35_17100EGA71_24270EGB62_21680EGD06_15715EGD16_14315EGD39_24895EGN78_09350EGS27_03185EGS35_19355EGS95_21800EGZ09_12750EGZ16_06515EGZ23_23875EGZ50_21920EGZ58_15400EH010_14325EH026_21195EH036_06640EH039_10025EH041_05435EH051_16110EH067_15470EH070_06970EH335_21915EH341_12735EH342_24755EH350_17345EH369_21640EH378_15930EH386_25230EH399_21155EH401_10685EH418_06845EH444_12285EHA18_22050EHB11_07790EHF48_17225EHF67_09490EHF90_06145EHG07_07050EHG24_07890EHG30_18460EHG48_24035EHG66_12975EHG70_20350EHG76_20165EHI00_08335EHJ84_14015EHJ86_02550EHN14_08740EHN63_14605EHN71_15590EHN75_12385EHO09_17885EHO38_12195EHT01_22920EHT09_10280EHT38_16585EHT47_05750EHT73_23755EHU13_16640EHU16_16550EHZ27_07140EHZ40_09155EHZ65_05630EHZ75_15375EHZ79_18100EI217_14130EIM38_05440EIN07_22950EIN82_06840EIP55_16565EIQ75_06550EIQ80_04200EIR00_03290EIR18_24230EIR32_12345EIR43_13825EIR57_11205EIR59_19445EIR69_14000EIR93_11695EIS98_21040EIT30_13990EIT86_05520EIU05_18685EIU30_20815EIU77_04460EIU90_12615EIV01_23550EIV03_23175EIV27_10450EKD96_19760F0673_16280F0756_22145F0896_19315F0902_22115F1527_14270F1G59_16865F1G81_21775F1G85_20630F1I31_00440F2082_15310F2102_17270F2108_16175F2139_18170F2199_03585F2262_15535F2C17_06680F2C56_05410F2D15_12435F2D26_09345F2E92_15465F2G12_18510F2G31_22925F2G76_06680F2G84_22785F2H66_18545F2I95_24090F3368_20685F3E97_20965F3V10_19415F6G03_09515F6G43_00040F6H70_21285F7450_00040F7I91_05580F7M71_13785F7T58_18355F8F58_04220FE35_12445FJR52_13185FLX20_09295FNG56_06900FQQ56_13745FQR50_24835FR099_18215FRJ97_19625FRK18_23550FRL07_18120FSD06_04200FZ154_15980FZ164_00030FZ353_00045FZ416_01190GB762_06020GC435_05775GC725_10640GC766_07220GCA81_24045GCH85_24895GCO23_04195GCR35_19115GFE88_17785IX01_18085LE63_20590LL78_16895XR15_15145XU42_00070XY76_00070YI00_24075

UniProt
Find proteins for Q6EAT3 (Salmonella enterica)
Explore Q6EAT3 
Go to UniProtKB:  Q6EAT3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-32B183Homo sapiensMutation(s): 0 
Gene Names: RAB32
UniProt & NIH Common Fund Data Resources
Find proteins for Q13637 (Homo sapiens)
Explore Q13637 
Go to UniProtKB:  Q13637
PHAROS:  Q13637
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.41α = 90
b = 67.41β = 90
c = 427.34γ = 120
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
German Research FoundationGermanySFB1035

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references