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- PDB-8qh2: Crystal structure of chimeric UAP1L1 -

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Basic information

Entry
Database: PDB / ID: 8qh2
TitleCrystal structure of chimeric UAP1L1
ComponentsUDP-N-acetylhexosamine pyrophosphorylase,UDP-N-acetylhexosamine pyrophosphorylase-like protein 1
KeywordsTRANSFERASE / Chimera / UAP1L1
Function / homology
Function and homology information


protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production / antiviral innate immune response ...protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production / antiviral innate immune response / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
UDP-N-acetylhexosamine pyrophosphorylase / UDP-N-acetylhexosamine pyrophosphorylase-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsChen, X. / Yan, K. / Bartual, S. / van Aalten, D.
Funding support United Kingdom, Denmark, 2items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
Novo Nordisk FoundationNNF21OC0065969 Denmark
CitationJournal: To Be Published
Title: UAP1L1 is an active pyrophosphorylase with an active site disulfide regulating protein thermostability
Authors: Chen, X. / Yan, K. / Bartual, S. / Ferenbach, A. / van Aalten, D.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylhexosamine pyrophosphorylase,UDP-N-acetylhexosamine pyrophosphorylase-like protein 1


Theoretical massNumber of molelcules
Total (without water)57,7141
Polymers57,7141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22820 Å2
Unit cell
Length a, b, c (Å)113.523, 113.523, 43.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein UDP-N-acetylhexosamine pyrophosphorylase,UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 / Antigen X / AGX / Sperm-associated antigen 2


Mass: 57713.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UAP1, SPAG2, UAP1L1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16222, UniProt: Q3KQV9, UDP-N-acetylgalactosamine diphosphorylase, UDP-N-acetylglucosamine diphosphorylase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic, pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.75→43.97 Å / Num. obs: 14923 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 78.64 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.6
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 2141 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158-000refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→41 Å / SU ML: 0.5079 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.6981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 672 4.51 %
Rwork0.2327 14233 -
obs0.2351 14905 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.45 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 0 0 3810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873898
X-RAY DIFFRACTIONf_angle_d1.06255274
X-RAY DIFFRACTIONf_chiral_restr0.0543566
X-RAY DIFFRACTIONf_plane_restr0.0094698
X-RAY DIFFRACTIONf_dihedral_angle_d18.04231465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.3831150.3872807X-RAY DIFFRACTION99.86
2.96-3.260.40251420.32272803X-RAY DIFFRACTION99.97
3.26-3.730.33351280.27782848X-RAY DIFFRACTION100
3.73-4.70.26851400.22112848X-RAY DIFFRACTION99.97
4.7-410.24121470.18292927X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05193609763-1.25544852506-0.1580138595931.79079657216-0.09943920316550.448079385037-0.8985189022590.826224049977-1.01011460804-0.2944214184941.616107826590.8336589255730.173775940059-0.2789866312930.7417305245320.242257819242-0.3784395786340.3455988894450.762801493783-0.2680058178631.34694933623-40.1961631648-56.7683310831-18.7775386695
20.11793256228-0.3313676083070.106292195282.512488629010.2144426634170.4113346787420.535906841031-0.444460689512-0.1625867795431.479758746830.2381702110750.125429601758-0.1436142905840.4949605810710.3479763878140.5736041783090.07672807554670.1897631136050.7205399170050.09559652715490.792325692549-40.1647132702-46.6556229148-3.66310882844
31.88870932490.0703692274785-0.1292776337590.08398405210430.02515316200910.04449657694610.0400507058325-1.12465094351-0.1233843212860.4273639010220.19242507120.2403464228260.347517732638-0.0256871238179-0.000739065868441.31557572343-0.0327754831677-0.2602457606320.6266881291220.0952849593010.661737525962-28.1839528544-21.817967607514.8153394513
40.005865088839710.0106119168122-0.009189105844710.0163827620906-0.01517312077660.0180001239305-0.149107757305-0.118384881596-0.0449206432012-0.1155697555130.113200556726-0.104535861232-0.1968473657190.152072089212-0.0003241137867051.62832548584-0.355777774909-0.4239694484561.12691469182-0.02057572917631.12619086452-3.21180259304-20.903371890918.0644486576
50.6774426757380.0178979491490.2992003321246.99260988009E-5-0.005220196303751.146912728880.230472348253-0.899091592845-0.3608400197851.08316380768-0.439617804062-0.255249827065-1.07907697161-0.0924086158720.5527907117751.01572986399-0.466995547642-0.7394581623920.7312046011790.3156794605880.927942599449-4.68912094633-35.925131164414.2425503212
6-0.009012834279940.01127976345440.001945333798970.018952787638-0.0221478894737-0.002606822164150.3863544682070.646783024003-0.4279389997330.31067209292-0.161775902947-0.1840596704810.1485285940410.06306208371810.000124854587670.5323389541160.11240074973-0.09203303231750.890793051028-0.3940487521770.893213573237-21.0428305837-34.5561754195-10.6071907016
70.506855882997-0.2046533824120.08962414426950.741210868224-0.07476281226070.0197065271987-0.2109306514661.21436418048-0.0401311879032-0.4518123063520.202916639711-0.441384288093-0.555590246669-1.027770746930.004135804641980.4949278744580.057737759103-0.1480163448480.976227354861-0.3405008758090.711788418629-8.46225174964-34.3940109509-13.4839910496
81.348776648440.542309182601-0.9545151440360.930350250794-0.2164409065360.6255916380470.6093537880310.141232040048-1.895200659320.718212313196-0.297460014829-0.9524609156710.316252837996-0.208653091669-0.3780048303740.6053255169290.064674935265-0.4459781222230.555407282461-0.126934364011.28050135087-5.49831594747-42.0876848718-1.03452200682
90.674169120403-0.00530423071141-0.01520064389831.32046495674-0.9628023373020.517295677023-0.4095234427581.09551725072-0.6243058217310.7525978237860.462969280697-0.4785686046680.125063604576-0.0801413511722-0.195896069050.445790779856-0.118301396182-0.1283924901960.595202096707-0.1861985792990.946305040733-24.2593167328-45.9850579926-5.41798201126
102.33132557268-0.246343013104-0.462820227990.003983038121850.001170077695740.09540218417610.8898820788170.0844421406001-0.9768187408290.774978832632-0.875856314769-0.399656595528-0.0150386343167-0.546073844498-0.2807475792471.03307299405-0.0387607682062-0.4928488840330.3902518137160.2143313263720.680102915964-12.3144217108-36.27379844319.49938664794
110.107949309887-0.00399717042511-0.01674083508310.4013069926520.1901315785780.2671032011890.3299541900110.0707565912954-0.08742274605641.30048673972-0.2295507550560.2393540873980.0942034496765-0.782783273499-0.01058771246541.14928393620.05183391234980.007412882762810.631922094370.07063104311010.462985987197-25.8034814787-21.16552273046.09830014981
120.0708517620426-0.0827916461783-0.07366118572960.08310752393470.08045165504040.076341527072-0.1178375815820.4161154762750.0162887091364-0.513053990476-0.281303000040.27448635804-0.170164512476-0.2188244952350.01833501952841.08905541065-0.204320368028-0.05454624024271.60861784586-0.06795912560730.444467558147-29.5552474093-26.27386832253.4306953503
130.117384620314-0.02687310808130.08239847310940.135877042750.0223486836140.05177226902620.4118038870540.3124450483790.89737836403-0.1130732008260.384887794051-0.1217770565540.447623246085-0.0985623291820.002633148301911.025215976330.120864042910.3377912970331.132829989010.4118687848310.928991592508-32.2700379586-15.09701652064.26797035164
140.0123963342709-0.0271924256052-0.01122434772370.04307366651870.02252201647330.01536862378590.272757408652-0.2606985974920.41887735796-0.334101915876-0.3442990276210.05681453067890.3973222782930.3890064877680.0008630708521560.790084476083-0.171754987985-0.06654358478480.8517679671210.09431687087181.17151041341-25.358328467-11.569922604810.3676743387
152.6023914522-0.6162918965950.3351978678490.784193431599-0.0132312917270.06277338080050.6655311793140.190993994669-0.7317041469290.869522927846-0.574198354570.121209477624-0.762504897247-0.556469206011-0.09802375978521.047081875810.119886180233-0.1025738593840.6479250758430.1051464260590.449463797899-23.6198598655-38.858728136410.4455016645
160.231927283506-0.309946924419-0.03653599291350.2726036116940.1129517782040.06736034691260.1377320305360.2202320205040.291726532015-0.789350650760.7819869818740.4125337698-0.342512455397-0.03896341441730.002766977089640.912579123091-0.2056466489090.07962499898570.9393778576890.1718546240570.900739344621-37.7987289098-35.9748650564-14.9586008396
173.4397012825-0.213028609375-0.07526256012250.6678767732050.1888609885110.1698080328031.010297412291.08111159681-0.1689990431420.867754666583-0.4618836661730.252024175261-0.341439614111-0.1787028362120.1737948669791.065757587890.0749052395004-0.09992353756920.5826588741680.0437707845970.453950301304-16.9409287386-26.1374165022-0.849180269492
182.14682097757-0.886564866854-0.7033332751790.6149261520151.006265777752.320380576290.2176400678510.5955645413770.9421880133190.120135717303-0.08383192426080.461229671317-1.367677528330.4665140650070.5597501357781.05311065404-0.303875952035-0.300195196960.8945020240180.03864207169710.6864351097925.32949905286-14.5955599181-5.59629584237
190.3041413085990.105094840499-0.8775185258290.148609949422-0.4825534050633.150682769970.7511279109510.163895025469-0.6116270482650.670470970073-0.06411174491650.445017190734-2.111253635340.04980290086281.252066744070.838948217883-0.279859756323-0.3989773562670.7524929041820.05265086445390.7380176803567.29416591791-23.6885716279-3.0414854696
200.241166168962-0.00434290502545-0.2090322851960.160007072468-0.004896969824140.183805106598-0.2645681650760.016765420465-0.148522211193-0.0458822977451-0.3093355759550.0160196169021-0.2846695944970.0382308578263-0.2998967319471.05371777991-0.305990504261-0.4831009848940.6924767783050.1760162713250.9823462583718.5080686505-28.9211405975-7.81664019494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid -3:34)-3 - 341 - 38
22(chain A and resid 35:55)35 - 5539 - 59
33(chain A and resid 56:80)56 - 8060 - 74
44(chain A and resid 84:89)84 - 8975 - 80
55(chain A and resid 90:109)90 - 10981 - 100
66(chain A and resid 110:119)110 - 119101 - 110
77(chain A and resid 120:139)120 - 139111 - 130
88(chain A and resid 140:183)140 - 183131 - 174
99(chain A and resid 184:239)184 - 239175 - 230
1010(chain A and resid 240:280)240 - 280231 - 271
1111(chain A and resid 281:301)281 - 301272 - 292
1212(chain A and resid 302:307)302 - 307293 - 298
1313(chain A and resid 308:318)308 - 318299 - 309
1414(chain A and resid 319:325)319 - 325310 - 316
1515(chain A and resid 326:351)326 - 351317 - 342
1616(chain A and resid 352:382)352 - 382343 - 373
1717(chain A and resid 383:428)383 - 428374 - 419
1818(chain A and resid 429:461)429 - 461420 - 442
1919(chain A and resid 462:490)462 - 490443 - 471
2020(chain A and resid 491:495)491 - 495472 - 476

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