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- PDB-6uek: Structure of Urocanate Hydratase from Trypanosoma cruzi in comple... -

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Basic information

Entry
Database: PDB / ID: 6uek
TitleStructure of Urocanate Hydratase from Trypanosoma cruzi in complex with NAD+
ComponentsUrocanate hydratase
KeywordsLYASE / Chagas disease / Urocanate Hydratase / NAD+ / Interdomain movement
Function / homology
Function and homology information


urocanate hydratase / urocanate hydratase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate
Similarity search - Function
Urocanase conserved site / Urocanase signature. / Urocanase / Urocanase, Rossmann-like domain / Urocanase, N-terminal domain / Urocanase, C-terminal domain / Urocanase superfamily / Urocanase, central domain superfamily / Urocanase Rossmann-like domain / Urocanase N-terminal domain / Urocanase C-terminal domain
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Imidazolonepropionate hydrolase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBoreiko, S. / Silva, M. / Melo, R.F.P. / Silber, A.M. / Iulek, J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)573607/2008-7 and 08/57910-0 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Structure of Urocanate Hydratase from the protozoan Trypanosoma cruzi.
Authors: Boreiko, S. / Silva, M. / de F P Melo, R. / Silber, A.M. / Iulek, J.
History
DepositionSep 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urocanate hydratase
B: Urocanate hydratase
C: Urocanate hydratase
D: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,4028
Polymers302,7484
Non-polymers2,6544
Water10,485582
1
A: Urocanate hydratase
B: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,7014
Polymers151,3742
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-56 kcal/mol
Surface area41370 Å2
MethodPISA
2
C: Urocanate hydratase
D: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,7014
Polymers151,3742
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-55 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.614, 134.788, 113.399
Angle α, β, γ (deg.)90.000, 93.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Urocanate hydratase


Mass: 75687.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D9S6
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, potassium dihydrogen phosphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.16→113.22 Å / Num. obs: 128119 / % possible obs: 94.3 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 15.52
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 9011 / CC1/2: 0.682 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWK

1uwk


Resolution: 2.16→113.22 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2546 --
Rwork0.2181 --
obs-128117 94.3 %
Displacement parametersBiso max: 179.33 Å2 / Biso mean: 51.8199 Å2 / Biso min: 20.22 Å2
Refinement stepCycle: final / Resolution: 2.16→113.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18338 0 176 582 19096
Biso mean--51.38 42.15 -
Num. residues----2543
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)
10.95910.1002-0.41831.2007-0.18290.37120.0081-0.1141-0.18560.1392-0.0464-0.29610.01950.08660.03250.27460.0153-0.03440.19840.02250.495537.40221.21111.487
21.4672-0.58740.31492.69240.91641.0085-0.0567-0.2842-0.3440.42710.0858-0.35210.17190.0315-0.03440.4002-0.00120.00490.22130.06220.584153.7552.877124.044
31.03740.07330.22130.9159-0.10350.71570.07760.0510.1902-0.0630.0298-0.2357-0.15110.0604-0.08240.2685-0.00810.06480.14680.02450.425936.10544.73899.58
41.1972-0.14280.09631.1912-0.12560.11810.13910.0180.3080.1168-0.0540.2786-0.1607-0.1229-0.05990.30090.05320.08250.22090.02540.40715.62948.344106.823
52.50760.59670.89071.69930.82953.8526-0.1776-0.3594-0.07050.3127-0.01310.34180.09930.10960.16790.38590.06530.10290.28140.08880.5135-10.27822.657128.317
61.5361-0.21710.0581.3749-0.24980.98980.01310.1357-0.2396-0.0452-0.02210.28950.1084-0.1913-0.00730.2282-0.0121-0.00250.1912-0.01230.38117.2422.068103.045
71.0484-0.37110.61810.7389-0.18222.78070.07030.2542-0.0724-0.27510.0476-0.2440.13910.6762-0.10340.39320.03070.070.5059-0.05820.364137.22429.48657.202
8-0.0012-0.0055-0.00920.46230.81291.4278-0.0515-0.45970.09331.17070.5478-0.51230.26940.4092-0.35871.16710.5046-0.08650.5263-0.25090.675730.251.61152.975
93.0065-0.93321.98132.89151.46762.97170.32381.02280.7425-0.1997-0.7804-1.25480.6240.38680.37390.80060.416-0.03061.150.03540.633942.6686.8250.744
102.8483-2.087-1.24286.23043.30611.76250.00590.0028-0.61191.235-0.21280.69450.42210.0210.26591.41980.2995-0.30090.4972-0.29581.013334.26-11.35942.708
114.6104-3.1761-6.05772.21594.13458.0134-0.14360.1504-0.2201-0.01120.0041-0.03710.2942-0.15360.24751.18690.3233-0.15470.636-0.35520.535430.9110.75533.592
124.37243.88141.08039.5719-1.77912.85180.1914-1.04180.2221.2195-0.4253-0.1171.21532.90030.20671.04320.3995-0.03341.3989-0.2450.559542.02218.45734.06
133.64661.84031.76176.74042.00321.06040.26650.4992-0.3244-0.1158-0.45610.2960.76730.12170.20441.13450.0943-0.10990.6694-0.22350.504227.5189.51830.245
148.01730.373-4.15829.0059-3.26994.66840.31250.5473-0.6094-1.41240.3648-1.142.72160.7808-0.66631.06230.170.0230.5837-0.07520.546521.37515.38135.895
152.5178-1.367-2.01525.84272.95592.8456-0.1654-0.0735-0.0911-0.01960.1862-0.37290.29190.1969-0.21521.06740.2855-0.18020.4923-0.22460.559134.62-0.8144.511
165.2948-5.532-4.90045.77955.11934.5396-1.5223-1.96950.01990.60731.74210.616-0.52190.9083-0.20041.21110.3827-0.13661.09030.02590.631334.2479.07249.444
170.8525-0.5386-0.79020.35310.63632.21070.1841-0.0454-0.0734-0.0915-0.1010.02070.0216-0.0365-0.12562.1067-0.3509-0.36310.63960.08940.616826.119-6.16253.377
188.14190.6873-6.57958.3248-5.44648.2099-0.53691.4002-1.8193-2.46650.9617-0.80792.39720.6066-0.26981.31150.0093-0.21781.1244-0.56380.867337.7020.77255.019
1925.78465.43479.40814.6524.6775-0.716-1.2210.2910.85920.93490.5267-0.3925-0.2787-0.17411.34170.7736-0.45471.3341-0.26911.128442.706-2.56237.828
209.6663-0.5116-1.01997.34243.90344.45290.54380.09050.3197-0.2235-0.0848-0.51841.1510.7348-0.35150.75530.2638-0.13360.655-0.11040.400531.64413.06538.291
213.86621.43990.38384.2824.6885.57460.08840.27281.20410.5503-0.9899-1.3683-0.41221.72510.84050.7055-0.0085-0.3540.94990.15891.622836.35624.31128.621
221.6473-0.7781-1.34334.13682.19171.73860.20770.2926-0.59820.19150.5813-0.64960.25990.3545-0.55671.3859-0.0389-0.27850.5639-0.2380.647120.1953.91740.859
235.1179-2.72515.41443.1242-2.97537.5661-0.4384-1.6645-0.78540.58610.12680.62731.6269-1.49460.45741.1694-0.01960.33660.77990.02880.465317.88211.00630.013
240.5481-0.2688-0.01270.464-0.08591.80570.2068-0.0753-0.2824-0.08780.08480.11260.8014-0.8051-0.26290.582-0.1773-0.07160.60280.06920.396917.54515.07965.122
250.9379-0.24650.42590.2075-0.22120.2775-0.0592-0.2384-0.00540.11690.0603-0.0415-0.0642-0.1262-0.15330.33890.2665-0.06891.572-0.04030.4662-13.92330.85964.904
261.3943-0.02610.23380.6448-0.20430.52610.30460.075-0.5294-0.0084-0.03740.00990.0809-0.70540.19230.3069-0.0836-0.16591.3556-0.04650.4515-8.34426.78645.281
273.85861.60260.59321.0710.21650.40690.03141.0131-0.6094-0.30040.3208-0.1190.06460.0591-0.15250.2205-0.0071-0.05081.2919-0.13480.535-14.4724.24744.078
280.04390.04470.01490.36120.06410.012-0.0009-0.45880.1367-0.5315-0.00210.2617-0.4805-1.30380.43680.31120.3752-0.05931.7405-0.06030.3906-1.57235.74157.236
293.4294-3.6059-0.33246.78590.09550.0984-0.071-0.0351-0.0137-0.0486-0.01420.0519-0.2357-0.1094-0.04971.38830.6897-0.23620.6818-0.14930.509711.47862.76551.791
301.40060.96710.82170.8997-0.52885.65890.2058-0.4533-0.12240.3126-0.1833-0.0729-0.233-0.5158-0.03091.47160.57780.20791.22810.31130.62213.07264.248.913
312.6350.37770.84330.45540.71091.1349-0.1044-0.75860.23990.01520.07460.00390.0322-0.26790.04830.4627-0.105-0.40570.95330.25271.1822-8.39660.62140.973
324.14630.8089-2.58360.158-0.50381.61060.44540.5531.21690.2620.57490.6462-1.147-0.7338-0.84271.62220.4363-0.12660.76270.09420.8591.08878.9240.411
335.8127-4.1557-1.48186.92952.24210.73110.60560.15-1.5056-1.5514-0.22260.78681.68910.4241-0.47981.34310.4218-0.44050.81630.12861.01226.07768.49630.586
347.38055.9934-5.57655.9003-2.58587.8607-0.4572-0.55231.2195-1.5751-0.80351.1772-0.9985-1.61921.22341.46960.5692-0.30021.174-0.29250.6934-2.14652.30822.88
350.7165-0.0932-0.38822.19681.11050.7198-0.48270.46510.2696-0.5558-0.31110.2535-1.4592-0.14750.39922.1588-0.3682-0.06120.8277-0.1190.495812.52161.61725.619
364.2028-4.60684.85825.0496-5.32515.6150.54791.412-0.359-1.4724-0.7244-0.0232-0.41290.14770.18430.9423-0.25290.00140.9805-0.09510.325117.40754.73130.771
370.47630.1132-0.7221.1616-1.30064.09280.23780.2717-0.18920.0035-0.1219-0.02050.9359-0.4689-0.15851.28190.4925-0.10371.123-0.09120.36081.95168.47440.498
384.72993.78340.21816.66691.79937.2611-0.50720.0231-0.6515-0.5593-0.03421.4659-1.2951-0.22970.47631.185-0.0614-0.00590.29690.0231.319414.11574.44150.814
390.9036-0.88542.5362.666-4.76372.00020.1124-0.1027-0.1424-0.07790.0832-0.15190.5790.3225-0.14581.3680.4592-0.25611.5936-0.24130.48962.09156.41543.117
405.0115-4.0866-0.35632-0.97196.45680.1660.29580.0288-0.1325-0.34540.3545-0.1893-0.3360.17520.87890.22910.07270.6722-0.33870.6126.18371.78251.743
418.5312-9.0824-4.10649.66874.37151.97650.0034-3.9563-2.73284.1315-0.15450.38213.315-2.25720.16411.5422-0.3985-0.19421.06710.20950.5945-5.16764.73346.965
423.71824.82040.02217.1072-2.42227.0021.589-3.0725-4.07890.23450.6571.51962.6729-1.2406-2.23861.0715-0.208-0.54612.03441.04132.3544-5.51272.05632.326
430.81030.76690.77580.82661.19462.61940.033-0.0538-0.126-0.429-0.30290.15570.5836-0.43280.19911.30710.25220.060.6054-0.01830.25846.93358.08532.547
448.0817-1.02043.49866.6079-7.16648.4940.1133-0.5349-0.8231-0.0116-0.10430.0953-0.02980.0797-0.01311.91870.4065-0.07010.80190.26250.93254.50748.57618.487
450.09850.0815-0.09470.1002-0.10180.1058-0.1711-0.06770.13180.0852-0.0096-0.0098-0.4576-0.08310.02381.4390.1918-0.05170.62680.04440.352115.0760.19340.104
468.8842-3.32711.93036.5541-2.97281.3733-0.5719-0.11180.08050.057-0.4101-0.39630.27143.33451.00861.1557-0.0394-0.12570.63320.22890.419519.80356.98737.714
475.924-1.03270.60282.95430.20270.8558-0.6385-0.50050.1472-0.15860.10880.1364-0.3699-0.30590.10411.02770.4824-0.06720.61540.00260.351914.13954.53359.861
481.0244-2.17580.33256.6208-1.76920.70690.0134-0.0397-0.32490.07230.19160.7544-0.1328-0.2329-0.16010.950.7195-0.18070.9878-0.15750.55041.20560.4171.127
490.2290.06850.09520.37170.32760.4449-0.088-0.19560.1375-0.17750.01770.0756-1.1999-0.7978-0.10130.70680.29690.00050.7072-0.0040.316416.77847.57962.674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:234 )A3 - 234
2X-RAY DIFFRACTION2( CHAIN A AND RESID 235:440 )A235 - 440
3X-RAY DIFFRACTION3( CHAIN A AND RESID 441:672 )A441 - 672
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:234 )B3 - 234
5X-RAY DIFFRACTION5( CHAIN B AND RESID 235:440 )B235 - 440
6X-RAY DIFFRACTION6( CHAIN B AND RESID 441:671 )B441 - 671
7X-RAY DIFFRACTION7( CHAIN C AND RESID 3:234 )C3 - 234
8X-RAY DIFFRACTION8( CHAIN C AND RESID 258:267 )C258 - 267
9X-RAY DIFFRACTION9( CHAIN C AND RESID 279:288 )C279 - 288
10X-RAY DIFFRACTION10( CHAIN C AND RESID 298:312 )C298 - 312
11X-RAY DIFFRACTION11( CHAIN C AND RESID 323:330 )C323 - 330
12X-RAY DIFFRACTION12( CHAIN C AND RESID 362:371 )C362 - 371
13X-RAY DIFFRACTION13( CHAIN C AND RESID 375:394 )C375 - 394
14X-RAY DIFFRACTION14( CHAIN C AND RESID 408:414 )C408 - 414
15X-RAY DIFFRACTION15( CHAIN C AND ( RESID 248:252 OR RESID 271:276 OR RESID 293:295 OR RESID 315:320 ) )C248 - 252
16X-RAY DIFFRACTION15( CHAIN C AND ( RESID 248:252 OR RESID 271:276 OR RESID 293:295 OR RESID 315:320 ) )C271 - 276
17X-RAY DIFFRACTION15( CHAIN C AND ( RESID 248:252 OR RESID 271:276 OR RESID 293:295 OR RESID 315:320 ) )C293 - 295
18X-RAY DIFFRACTION15( CHAIN C AND ( RESID 248:252 OR RESID 271:276 OR RESID 293:295 OR RESID 315:320 ) )C315 - 320
19X-RAY DIFFRACTION16( CHAIN C AND RESID 253:257 )C253 - 257
20X-RAY DIFFRACTION17( CHAIN C AND RESID 268:270 )C268 - 270
21X-RAY DIFFRACTION18( CHAIN C AND RESID 289:292 )C289 - 292
22X-RAY DIFFRACTION19( CHAIN C AND RESID 296:297 )C296 - 297
23X-RAY DIFFRACTION20( CHAIN C AND RESID 340:361 )C340 - 361
24X-RAY DIFFRACTION21( CHAIN C AND RESID 372:374 )C372 - 374
25X-RAY DIFFRACTION22( CHAIN C AND RESID 395:407 )C395 - 407
26X-RAY DIFFRACTION23( CHAIN C AND RESID 415:421 )C415 - 421
27X-RAY DIFFRACTION24( CHAIN C AND RESID 441:666 )C441 - 666
28X-RAY DIFFRACTION25( CHAIN D AND RESID 8:16 )D8 - 16
29X-RAY DIFFRACTION26( CHAIN D AND RESID 19:58 )D19 - 58
30X-RAY DIFFRACTION27( CHAIN D AND RESID 60:73 )D60 - 73
31X-RAY DIFFRACTION28( CHAIN D AND RESID 75:220 )D75 - 220
32X-RAY DIFFRACTION29( CHAIN D AND RESID 221:237 )D221 - 237
33X-RAY DIFFRACTION30( CHAIN D AND RESID 258:267 )D258 - 267
34X-RAY DIFFRACTION31( CHAIN D AND RESID 279:288 )D279 - 288
35X-RAY DIFFRACTION32( CHAIN D AND RESID 298:312 )D298 - 312
36X-RAY DIFFRACTION33( CHAIN D AND RESID 323:328 )D323 - 328
37X-RAY DIFFRACTION34( CHAIN D AND RESID 362:371 )D362 - 371
38X-RAY DIFFRACTION35( CHAIN D AND RESID 375:393 )D375 - 393
39X-RAY DIFFRACTION36( CHAIN D AND RESID 408:414 )D408 - 414
40X-RAY DIFFRACTION37( CHAIN D AND ( RESID 248:252 OR RESID 271:276 OR RESID 295:295 OR RESID 315:320 ) )D248 - 252
41X-RAY DIFFRACTION37( CHAIN D AND ( RESID 248:252 OR RESID 271:276 OR RESID 295:295 OR RESID 315:320 ) )D271 - 276
42X-RAY DIFFRACTION37( CHAIN D AND ( RESID 248:252 OR RESID 271:276 OR RESID 295:295 OR RESID 315:320 ) )D295
43X-RAY DIFFRACTION37( CHAIN D AND ( RESID 248:252 OR RESID 271:276 OR RESID 295:295 OR RESID 315:320 ) )D315 - 320
44X-RAY DIFFRACTION38( CHAIN D AND RESID 238:247 )D238 - 247
45X-RAY DIFFRACTION39( CHAIN D AND RESID 253:257 )D253 - 257
46X-RAY DIFFRACTION40( CHAIN D AND RESID 268:270 )D268 - 270
47X-RAY DIFFRACTION41( CHAIN D AND RESID 289:292 )D289 - 292
48X-RAY DIFFRACTION42( CHAIN D AND RESID 296:297 )D296 - 297
49X-RAY DIFFRACTION43( CHAIN D AND RESID 338:361 )D338 - 361
50X-RAY DIFFRACTION44( CHAIN D AND RESID 372:374 )D372 - 374
51X-RAY DIFFRACTION45( CHAIN D AND RESID 400:407 )D400 - 407
52X-RAY DIFFRACTION46( CHAIN D AND RESID 415:440 )D415 - 440
53X-RAY DIFFRACTION47( CHAIN D AND RESID 441:457 )D441 - 457
54X-RAY DIFFRACTION48( CHAIN D AND RESID 462:474 )D462 - 474
55X-RAY DIFFRACTION49( CHAIN D AND RESID 489:667 )D489 - 667

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