7UAU

The crystal structure of the K137A mutant of E. coli YGGS in complex with PLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability.

Tramonti, A.Ghatge, M.S.Babor, J.T.Musayev, F.N.di Salvo, M.L.Barile, A.Colotti, G.Giorgi, A.Paredes, S.D.Donkor, A.K.Al Mughram, M.H.de Crecy-Lagard, V.Safo, M.K.Contestabile, R.

(2022) Protein Sci 31: e4471-e4471

  • DOI: https://doi.org/10.1002/pro.4471
  • Primary Citation of Related Structures:  
    7U9C, 7U9H, 7UAT, 7UAU, 7UAX, 7UB4, 7UB8, 7UBP, 7UBQ

  • PubMed Abstract: 

    The pyridoxal 5'-phosphate (PLP) homeostasis protein (PLPHP) is a ubiquitous member of the COG0325 family with apparently no catalytic activity. Although the actual cellular role of this protein is unknown, it has been observed that mutations of the PLPHP encoding gene affect the activity of PLP-dependent enzymes, B 6 vitamers and amino acid levels. Here we report a detailed characterization of the Escherichia coli ortholog of PLPHP (YggS) with respect to its PLP binding and transfer properties, stability, and structure. YggS binds PLP very tightly and is able to slowly transfer it to a model PLP-dependent enzyme, serine hydroxymethyltransferase. PLP binding to YggS elicits a conformational/flexibility change in the protein structure that is detectable in solution but not in crystals. We serendipitously discovered that the K36A variant of YggS, affecting the lysine residue that binds PLP at the active site, is able to bind PLP covalently. This observation led us to recognize that a number of lysine residues, located at the entrance of the active site, can replace Lys36 in its PLP binding role. These lysines form a cluster of charged residues that affect protein stability and conformation, playing an important role in PLP binding and possibly in YggS function.


  • Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal phosphate homeostasis protein234Escherichia coliMutation(s): 1 
Gene Names: 
yggSyggS_1A5U30_002536A6592_01605A8499_002487A9X72_04235AAG43_002119ABE90_008885ACN81_19285ACU57_02420AM464_06455APX88_16445AT335_001847AW119_01715AWP93_03370B6R31_003812B6R48_004381B6R87_004199BANRA_03839BANRA_04036BF481_004825BFL24_20630BG944_003862BGZ_03731BHS81_17785BIZ41_00110BJI68_00120BMC79_000896BMT50_14985BMT91_06560BN17_28641BO068_000828BON63_07220BON64_00505BON66_18090BON67_07075BON68_25380BON69_08055BON71_16625BON72_22075BON73_20790BON74_12080BON75_05715BON76_19600BON77_06680BON78_02935BON79_04735BON80_08660BON84_07605BON87_03690BON88_27660BON89_07800BON90_06555BON91_21215BON92_03035BON93_14700BON94_11530BON95_23425BON96_08755BON97_01525BON98_24335BR158_001158BSR05_00525BTQ06_15305BvCmsF30A_00775BvCmsHHP019_01430BvCmsKKP036_00786BvCmsKSNP073_01009BvCmsNSP072_00005BVL39_11960C2121_000334C2U48_19125C3F40_21750C5N07_11350C5Y87_01815C9114_13755C9160_19505C9E67_04785CCS08_04675CDC27_15720CDL36_11990CG692_04170CG831_001596CIG67_09495CO706_12770COD53_12020CR538_04470CR539_19790CWS33_02090CXJ73_003041D3822_03980D3G36_06505D3Y67_09635D9D77_01715D9E34_07450D9H94_01780D9J61_17485DAH19_03655DAH20_07105DAH21_16420DAH22_01755DAH23_02545DAH24_02555DAH25_06525DAH26_02550DAH27_13005DAH28_14020DAH29_07970DAH30_03695DAH31_07445DAH32_08165DAH33_07600DAH36_04450DAH38_14410DAH40_03245DAH41_08800DAH42_03480DAH43_04295DAH45_02570DAH46_04290DAH47_01830DAH48_00100DAH49_05945DAH50_00985DEN87_23415DEN88_15345DEN89_15360DEN90_09900DEN93_01895DEN94_02765DEN95_05305DEN96_03260DEN97_02915DEN98_02920DEN99_00275DEO00_02260DEO01_06395DEO02_04040DEO03_09945DEO04_01960DEO05_01955DEO06_10490DEO07_10895DEO08_05235DEO09_01960DEO10_03860DEO11_03875DEO12_19480DEO13_03715DEO14_14565DEO15_02570DEO17_09170DEO18_08415DEO19_02695DEO20_04970DIV22_04725DM870_04190DN627_06500DNQ45_04905DRW19_08955DS732_21845DTL43_08565DTM16_23260DTM45_03435DU321_13160DXT69_09050DXT70_01070DXT73_11060E0I42_19975E2113_22350E2114_23105E2115_25170E2116_22045E2117_06585E2118_25780E2119_17460E2120_22990E2121_10340E2123_21170E2124_21650E2125_22595E2127_08790E2128_15520E2129_10865E2130_22720E2132_07800E2134_10685E2136_04185E5M02_18275E5P22_07505E5P23_16320E5P24_19370E5P25_09260E5P30_04575E5P31_12580E5P32_10610E5P35_01370E5P36_03040E5P37_15605E5P39_18620E5P40_16160E5P41_17595E5P42_03955E5P43_17815E5P44_03755E5P45_15495E5P46_17265E5P47_15135E5P48_16110E5P49_09785E5P50_06510E5P51_14720E5P52_04945E5S34_19085E5S35_06260E5S36_16600E5S37_19475E5S38_02910E5S39_05640E5S42_02315E5S43_06610E5S44_08370E5S46_03050E5S47_04035E5S48_19765E5S51_01045E5S52_07370E5S53_08955E5S55_07915E5S56_10495E5S57_01375E5S58_01605E5S61_06985E5S62_00685EA435_13755EAI46_13050EAN77_06340EAX79_18760EBP16_03495EC3234A_50c00850EC95NR1_02249ECs3826ED648_12865EHD79_07725EHH55_19850EI021_05995EIZ93_04705EKI52_19505EL79_0770EL80_0765ELT16_22100ELT20_11815ELT21_06930ELT24_14260ELT25_23905ELT26_01120ELT27_12075ELT29_11660ELT30_23070ELT32_11085ELT34_21400ELT35_11005ELT36_22555ELT39_24285ELT40_23250ELT44_23345ELT45_23015ELT46_09740ELT48_18535ELT51_11245ELT54_23985ELT55_20860ELT59_22130ELT60_23295ELT61_23190ELT63_22530ELT72_21945ELU07_18210ELU82_21625ELU88_08890ELU89_22125ELU90_06760ELU91_22220ELU94_16485ELU96_24085ELU97_24105ELU98_16800ELV00_09650ELV01_14635ELV02_23710ELV03_14355ELV04_23130ELV05_13450ELV07_18185ELV08_03735ELV09_05255ELV11_25160ELV12_21430ELV13_23925ELV20_21495ELV21_16555ELV22_07885ELV23_09990ELV24_22210ELV29_20480ELX56_22225ELX61_10855ELX68_21270ELX70_06600ELX79_17745ELX83_22385ELX85_03700ELY02_06930ELY05_01540ELY23_22015ELY24_21105ELY36_14265ELY39_02230ELY48_11860ELY50_05765EPS76_23030ERS085406_01321EVY14_04185EXX13_15075EYV17_01965EYV18_21555EYX47_12185F0L67_07365F2N31_22060F7F11_00195F9S76_07455F9S83_14710F9V24_03870F9X20_25345FE587_00885FEJ01_00445FFF58_11750FJQ51_10270FKO60_04535FOI11_01810FOI11_021370FPI65_18190FQ007_01470FQF29_10150FTV90_24115FTV92_22795FTV93_22815FV293_10555FVB16_24045FY127_17985FZN31_04490G3565_13830G5632_06490G9448_18855GIB53_14050GKF86_09175GKF89_08035GKG12_00085GNO40_18860GNZ05_07955GP650_01920GP662_19735GP946_14015GP954_13245GP979_21920GQE64_15305GQF59_22030GQM04_18765GQM09_03895GQM13_07895GQW68_13910GQW80_01115GRC73_21480GRW05_17975GRW57_26645GRW81_17185GTP88_07945GUB08_20850GUB92_14665GUC01_11340GUI33_09255HHH44_003830HI055_000095HKA49_003353HL563_05490HLV18_01610HLZ50_19300HMU06_00730HMU48_04490HMV41_05740HMV95_09385HV209_16500HV209_28430HVV39_06655HVW19_10795HVW43_21550HVX16_04630HVX32_17080HVY77_04590HVZ71_04370HX136_04100I6H00_22940I6H01_08680I6H02_10245IAI11_03475IH768_06245IH772_17565IT029_002518J0541_004081J4S20_003608J5U05_000108JE86ST02C_34240JE86ST05C_34280JFD_01472JNP96_22325NCTC10082_03252NCTC10089_00898NCTC10090_03953NCTC10418_01404NCTC10429_01490NCTC10865_01122NCTC10958_00951NCTC10974_01056NCTC11126_04786NCTC11181_03104NCTC12950_01061NCTC13148_02921NCTC13216_00987NCTC4450_02839NCTC7928_01950NCTC8008_00336NCTC8009_02182NCTC8179_06415NCTC8333_00986NCTC8450_05416NCTC8959_02664NCTC8985_05487NCTC9036_00912NCTC9037_01055NCTC9045_01016NCTC9111_01297NCTC9117_01392NCTC9775_04646ND22_003843RG28_06665SAMEA3472044_02854SAMEA3472067_03679SAMEA3472080_03697SAMEA3472147_01446SAMEA3751407_00781SAMEA3752557_03404TUM18780_07680WP2S18E08_09360WP4S18E07_08580

UniProt
Find proteins for P67080 (Escherichia coli (strain K12))
Explore P67080 
Go to UniProtKB:  P67080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67080
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.802α = 90
b = 124.802β = 90
c = 82.317γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
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 StatesR01GM129793
Other governmentUnited StatesS10OD021756

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.2: 2022-09-28
    Changes: Database references
  • Version 1.3: 2022-10-26
    Changes: Database references
  • Version 1.4: 2022-11-09
    Changes: Database references
  • Version 1.5: 2023-10-18
    Changes: Data collection, Refinement description