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- PDB-7ctm: Crystal structure of Thermotoga maritima alpha-glucuronidase (TM0... -

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Basic information

Entry
Database: PDB / ID: 7ctm
TitleCrystal structure of Thermotoga maritima alpha-glucuronidase (TM0752) in complex with NADH and D-glucuronic acid
ComponentsAlpha-glucosidase, putative
KeywordsHYDROLASE / Glycosyl hydrolase family 4 / NAD(P)-binding Rossmann-fold domain / LDH C-terminal domain-like / hydrolase activity / alpha-glucuronidase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / ISOPROPYL ALCOHOL / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsManoj, N. / Mohapatra, B.S.
CitationJournal: Biochem.J. / Year: 2021
Title: Structural basis of catalysis and substrate recognition by the NAD(H)-dependent alpha-d-glucuronidase from the glycoside hydrolase family 4.
Authors: Mohapatra, S.B. / Manoj, N.
History
DepositionAug 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8484
Polymers56,9281
Non-polymers9203
Water7,728429
1
A: Alpha-glucosidase, putative
hetero molecules

A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6958
Polymers113,8562
Non-polymers1,8396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2990 Å2
ΔGint-14 kcal/mol
Surface area34960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.150, 80.590, 88.630
Angle α, β, γ (deg.)90.000, 102.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-glucosidase, putative


Mass: 56927.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0752 / Plasmid: pMH2T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WZL1
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14 % PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole with pH 5.8, 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→36.8 Å / Num. obs: 40918 / % possible obs: 94.2 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.049 / Rrim(I) all: 0.133 / Net I/σ(I): 12.5 / Num. measured all: 295957 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.897.20.8682.326140.6860.340.93389.6
8.68-36.87.10.02240.944110.010.02498

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.30data scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KCX

6kcx


Resolution: 1.85→36.798 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 2005 4.9 %Random
Rwork0.1523 38909 --
obs0.1545 40914 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.02 Å2 / Biso mean: 26.2845 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 1.85→36.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 105 429 4332
Biso mean--25.97 31.15 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89630.32331210.2577264990
1.8963-1.94750.27521290.2338264090
1.9475-2.00480.24051260.1972265490
2.0048-2.06950.23511250.1687266590
2.0695-2.14350.2141280.1636267591
2.1435-2.22930.18661580.1552268592
2.2293-2.33080.19211490.1421274393
2.3308-2.45360.19941250.1472281595
2.4536-2.60730.21671530.1498283996
2.6073-2.80860.1951400.1515284497
2.8086-3.09110.20681560.1544290098
3.0911-3.5380.18851580.1432289498
3.538-4.45630.15111730.1181291599
4.4563-36.790.18241640.1448299199
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)
11.9556-0.56090.38532.01560.31561.34340.08240.3355-0.026-0.4477-0.11920.1922-0.1251-0.19040.01960.30110.0353-0.02050.2673-0.00320.12620.97213.398588.5375
20.5592-0.26490.09141.7855-1.18882.20330.05990.1453-0.0416-0.27-0.0603-0.04560.05410.14450.00960.14030.00730.01950.1459-0.03220.122910.412-4.5801103.2355
32.9423-0.9458-0.87760.4554-0.10142.045-0.00960.2053-0.0334-0.23110.02850.0468-0.0906-0.0282-0.01450.166-0.0028-0.00710.0555-0.00260.11312.15465.6354108.9191
40.994-0.16740.22951.22390.03710.921-0.00480.0016-0.1303-0.08050.01880.33610.0336-0.2321-0.01350.0807-0.0042-0.00770.1410.00690.1728-13.3518-5.41119.1053
50.2389-0.0285-0.48820.1215-0.0631.1240.01610.2519-0.0979-0.3561-0.06840.12160.0433-0.35170.0650.32160.0213-0.07510.2722-0.06710.2118-4.7661-1.560494.281
61.2418-0.05650.23041.0746-0.96172.7340.05090.01870.1667-0.0382-0.05580.0919-0.3622-0.09380.0040.15840.03540.00570.086-0.01110.1406-1.928111.6096120.1552
70.6152-0.1895-0.03521.94560.57661.71740.02810.0943-0.0739-0.134-0.034-0.17760.14650.17390.01350.08780.02290.01550.1202-0.01560.118317.2623-9.6476118.6063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )A1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 149 )A58 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 193 )A150 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 297 )A194 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 366 )A298 - 366
6X-RAY DIFFRACTION6chain 'A' and (resid 367 through 408 )A367 - 408
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 468 )A409 - 468

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