8EYZ

Engineered glutamine binding protein bound to GLN and a cobaloxime ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Engineering a Conformationally Switchable Artificial Metalloprotein.

Fatima, S.Boggs, D.G.Ali, N.Thompson, P.J.Thielges, M.C.Bridwell-Rabb, J.Olshansky, L.

(2022) J Am Chem Soc 144: 21606-21616

  • DOI: https://doi.org/10.1021/jacs.2c08885
  • Primary Citation of Related Structures:  
    8EYZ

  • PubMed Abstract: 

    Many naturally occurring metalloenzymes are gated by rate-limiting conformational changes, and there exists a critical interplay between macroscopic structural rearrangements of the protein and subatomic changes affecting the electronic structure of embedded metallocofactors. Despite this connection, most artificial metalloproteins (ArMs) are prepared in structurally rigid protein hosts. To better model the natural mechanisms of metalloprotein reactivity, we have developed conformationally switchable ArMs (swArMs) that undergo a large-scale structural rearrangement upon allosteric effector binding. The swArMs reported here contain a Co(dmgH) 2 (X) cofactor (dmgH = dimethylglyoxime and X = N 3 - , H 3 C - , and i Pr - ). We used UV-vis absorbance and energy-dispersive X-ray fluorescence spectroscopies, along with protein assays, and mass spectrometry to show that these metallocofactors are installed site-specifically and stoichiometrically via direct Co-S cysteine ligation within the Escherichia coli glutamine binding protein (GlnBP). Structural characterization by single-crystal X-ray diffraction unveils the precise positioning and microenvironment of the metallocofactor within the protein fold. Fluorescence, circular dichroism, and infrared spectroscopies, along with isothermal titration calorimetry, reveal that allosteric Gln binding drives a large-scale protein conformational change. In swArMs containing a Co(dmgH) 2 (CH 3 ) cofactor, we show that the protein stabilizes the otherwise labile Co-S bond relative to the free complex. Kinetics studies performed as a function of temperature and pH reveal that the protein conformational change accelerates this bond dissociation in a pH-dependent fashion. We present swArMs as a robust platform for investigating the interplay between allostery and metallocofactor regulation.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid ABC transporter substrate-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
229Escherichia coliMutation(s): 2 
Gene Names: 
glnHA5U30_004091A6592_04880A8499_000176A9X72_16950AAG43_003583ACN68_16860ACN81_02400ACU57_05845AF998_000125AM464_21485APX88_17575AT335_000554AT845_002764AW118_24500AW119_03915AWP47_29145B6R12_003536B6R15_002883B6R31_003222B6R48_003973B6R87_003886BANRA_01322BANRA_01764BEA19_14205BER14_07540BF481_003043BG944_004267BGM66_000966BHS81_04935BJI68_11495BJJ90_17825BK292_21345BK383_19105BLM69_000575BMC79_000611BMT49_05685BMT50_00560BMT91_20520BN17_06101BO068_000746BOH76_16995BON63_24725BON64_24190BON65_04740BON66_07455BON67_25290BON68_02720BON69_08400BON70_24775BON71_14305BON72_22420BON73_01195BON74_14830BON75_15470BON76_25420BON77_09375BON78_20655BON79_20060BON80_12630BON81_19085BON82_15305BON83_05500BON84_13940BON86_21740BON87_16800BON88_07465BON89_22820BON90_14295BON91_21900BON92_22285BON93_04225BON94_25770BON95_05775BON96_27115BON97_10525BON98_19710BR158_002878BRV02_000648BSR05_11095BTB68_001717BTQ06_26205BUO55_004168BvCmsF30A_02312BvCmsHHP019_04964BvCmsKKP061_03133BvCmsKSNP073_02686BVL39_24445BXT93_09325BZL69_00955C0P57_004641C1Q91_004053C2121_002453C2M16_01565C2R31_002978C2U48_05980C3F40_08525C5N07_02720C5Y87_11455C9114_21285C9160_24490C9E67_21255C9Z68_13890CA593_25060CCS08_19690CCV12_002704CDC27_03365CDL36_05995CDL37_06170CF22_003152CG831_000699CHM61_001352CIG67_24135CO706_26845CQ986_002219CR538_17365CR539_08495CR628_003110CTR35_001347CV83915_00768CWS33_06680CX938_000617CXJ73_000498CY655_04230D0X26_05085D1912_20655D1H34_001169D3822_09995D3C88_05045D3G36_03255D3Y67_17015D4N09_12520D4U49_00030D9D43_04855D9D77_09815D9E34_09280D9E49_16110D9H94_11690D9J03_11000D9J61_05355DAH17_03825DAH18_19240DAH19_07490DAH20_21020DAH21_16625DAH22_20195DAH23_12545DAH24_12625DAH25_13880DAH26_12570DAH27_27195DAH28_26570DAH29_21215DAH30_24830DAH31_23660DAH32_25755DAH33_16740DAH34_00565DAH35_19590DAH36_01785DAH37_00035DAH38_23920DAH40_16855DAH41_26115DAH42_14420DAH43_13740DAH45_14115DAH46_16030DAH47_10645DAH48_08930DAH49_15255DAH50_02775DD762_19985DEN86_16580DEN87_25365DEN88_18460DEN89_18240DEN90_15895DEN91_18520DEN92_25370DEN93_25685DEN94_25170DEN95_25645DEN96_14460DEN97_05945DEN98_14610DEN99_03305DEO00_15605DEO01_16930DEO02_15845DEO03_02745DEO04_17445DEO05_17315DEO06_16065DEO07_16850DEO08_10875DEO09_17170DEO10_17430DEO11_17320DEO12_17235DEO13_25310DEO14_25015DEO15_18570DEO17_18420DEO18_14095DEO19_25855DEO20_09480DIV22_24420DKP82_24310DM870_16080DN627_03140DNX30_21735DRW19_18320DS732_09030DTL43_10730DTL90_03445DTM45_05760DU321_00670DXT69_17235DXT70_03865DXT71_08710DXT73_10050E0I42_20880E2112_02675E2113_01945E2114_18730E2115_17055E2116_04330E2117_24095E2118_16300E2119_12420E2120_04215E2121_18185E2122_15175E2123_15570E2124_10840E2125_18565E2127_00470E2128_04955E2129_10405E2130_05520E2131_16230E2132_01450E2133_04840E2134_04965E2135_16085E2136_14980E2646_20010E3O05_01530E4K51_02810E4T14_00550E4T84_17465E5H86_25390E5M02_22525E5P22_03440E5P23_09650E5P24_07820E5P25_14380E5P26_02375E5P27_03730E5P28_05135E5P29_02255E5P30_11875E5P31_05030E5P32_00405E5P33_13470E5P34_03095E5P35_02485E5P36_15665E5P37_20315E5P39_19970E5P40_02695E5P41_16665E5P42_12050E5P43_17005E5P44_18530E5P45_22380E5P46_16045E5P47_19935E5P48_15405E5P49_19430E5P50_22740E5P51_16920E5S34_18760E5S35_18835E5S36_04930E5S37_23235E5S38_16415E5S39_18510E5S43_19010E5S44_19440E5S45_23380E5S46_22040E5S47_18610E5S48_18775E5S51_14615E5S52_10650E5S53_16880E5S54_25355E5S55_16870E5S56_20090E5S57_09335E5S58_12745E5S61_14780E5S62_04320E6C80_01100E6D34_16620EA239_02055EA435_03075EAI46_17535EAN77_08520EAX79_16230EC1094V2_3069EC95NR1_05084ECs0889ED648_06680EHD79_17160EI021_00555EIA08_01310EIZ93_04910EKI52_06410EL79_3071EL80_3032ELT16_02415ELT17_17330ELT20_02820ELT21_01480ELT22_07560ELT23_02015ELT24_02785ELT25_04925ELT26_09185ELT27_07495ELT28_15430ELT29_09190ELT30_04155ELT31_02235ELT32_01320ELT33_01125ELT34_02155ELT35_01150ELT36_07860ELT38_02015ELT39_12720ELT40_06625ELT41_10995ELT44_00485ELT45_07655ELT46_05645ELT48_02765ELT49_11575ELT50_00370ELT51_04720ELT52_01735ELT54_03790ELT55_02630ELT56_04370ELT58_13405ELT59_01975ELT60_02685ELT61_00525ELT63_00400ELT72_09395ELU07_01290ELU82_01275ELU83_00030ELU85_01090ELU88_02755ELU89_06090ELU90_16660ELU91_09660ELU94_20245ELU95_04135ELU96_01710ELU97_02075ELU98_07325ELU99_17975ELV00_00990ELV01_02685ELV02_04500ELV03_02685ELV04_09130ELV05_01070ELV07_02685ELV08_05490ELV09_09705ELV10_03635ELV11_00495ELV12_17700ELV13_05135ELV15_08005ELV16_06920ELV20_01690ELV21_07280ELV22_03390ELV23_04940ELV26_19830ELV28_13395ELV29_14030ELV40_13070ELX48_20960ELX61_08885ELX66_13645ELX68_03535ELX69_04805ELX76_06605ELX79_08650ELX85_04825ELX96_24945ELY02_21695ELY32_15660ELY36_07870ELY39_10000ELY41_22740ELY48_10875EN85_004581ERS085406_04011ERS139208_02685EWK56_11475ExPECSC038_02876EXX13_17615EYV17_11920EYV18_03835F0L67_04275F2N20_02135F2N31_03410F3N40_12265F7F11_11485F7N46_08470F9413_07780F9461_01305F9B07_02710F9S83_08475F9V24_04485F9X20_12650FDM60_08540FE584_14605FE587_14715FEJ01_13600FFF58_04660FGG80_18845FHO90_02740FHQ91_05095FIJ20_11900FJQ40_17745FJQ51_03360FJQ53_08590FKO60_07285FOI11_009340FOI11_10705FPI65_04950FPJ29_13820FPS11_01585FQF29_02765FV293_02200FVB16_07150FWK02_14955FY127_05225FZC17_24290FZN31_16475FZU14_07000G3813_001838G3V95_03410G3W53_12740G4A38_09725G4A47_02555G5603_02180G7630_000206G9448_06715GAI66_11760GAI89_13630GAJ12_17235GAJ26_02185GF147_05165GF699_09700GFY34_01840GIB53_03185GJ11_04510GJO56_05855GKF66_09425GKF89_13835GNW61_02415GNZ05_09120GOP25_10140GP711_00870GP944_02795GP965_17210GP979_15650GQM04_08380GQM13_17840GQM21_08920GQN34_06325GQW07_06480GQW68_09320GQW80_16390GRC73_03245GRO95_00200GRW05_01550GRW24_15895GRW56_11730GRW57_13110GSM54_17415GSY44_21500GTP88_11170GUC01_03260GUI33_12255H0O37_11575H0O39_10830H0O72_02630HEP30_007075HEP34_000682HHH44_004674HI055_001651HIE29_000308HIN64_003897HJQ60_003183HJU54_001291HKA49_004171HL563_07185HL601_10425HLV18_05320HLX92_21635HLZ50_00225HmCms169_02183HMJ82_04430HMV95_02550HMW38_01730HNC36_00575HNC59_02155HNC66_13445HNC99_06490HND12_01310HV109_16015HV209_04855HVV39_21020HVW04_06960HVW19_18030HVW43_08305HVY77_17775HVZ71_16640HX136_17495I6H00_09980I6H01_21610I6H02_22350IA00_002027IFB95_003951IH768_00950IH772_11995IT029_003785J0541_000988J4S20_005071J5U05_002124JE86ST02C_09210JE86ST05C_09750JFD_02409JNP96_08670NCTC10082_05067NCTC10089_03418NCTC10090_00382NCTC10418_05048NCTC10429_05756NCTC10865_04252NCTC11181_00607NCTC12950_03687NCTC13127_04610NCTC13216_03355NCTC4450_03842NCTC7922_06781NCTC7927_03810NCTC7928_05513NCTC8008_02951NCTC8009_06196NCTC8179_02263NCTC8333_03962NCTC8450_01827NCTC8500_03700NCTC8621_03555NCTC8959_00379NCTC8960_00488NCTC9001_01370NCTC9036_03440NCTC9037_03540NCTC9075_04560NCTC9111_03455NCTC9702_03882NCTC9706_00702NCTC9775_01675NCTC9777_03409NCTC9962_02368ND22_002874RG28_00455SAMEA3472044_00248SAMEA3472056_00231SAMEA3472147_02754SAMEA3751407_00314SAMEA3752557_02233SAMEA3753106_00906TUM18780_29030WP4S18E07_30170WR15_25350XU56_002013

UniProt
Find proteins for P0AEQ3 (Escherichia coli (strain K12))
Explore P0AEQ3 
Go to UniProtKB:  P0AEQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEQ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X5Z (Subject of Investigation/LOI)
Query on X5Z

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
FA [auth G]
KA [auth H]
M [auth A]
AA [auth E],
CA [auth F],
FA [auth G],
KA [auth H],
M [auth A],
MA [auth I],
Q [auth B],
QA [auth J],
RA [auth K],
T [auth C],
TA [auth L],
W [auth D]
AZIDOBIS (DIMETHYLGLYOXIMATO) PYRIDINECOBALT
C15 H23 Co N8 O4
KKXSWROVWVQWSY-GLPMUSQESA-N
GLN
Query on GLN

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
JA [auth G]
LA [auth H]
NA [auth I]
BA [auth E],
EA [auth F],
JA [auth G],
LA [auth H],
NA [auth I],
P [auth A],
PA [auth J],
S [auth B],
SA [auth K],
UA [auth L],
V [auth C],
Z [auth D]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
GA [auth G]
HA [auth G]
IA [auth G]
N [auth A]
O [auth A]
GA [auth G],
HA [auth G],
IA [auth G],
N [auth A],
O [auth A],
OA [auth J],
R [auth B],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth F],
X [auth D],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.125α = 90
b = 136.091β = 90.16
c = 150.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM138138

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-02-14
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary