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- PDB-5jy7: Complex of Mycobacterium smegmatis trehalose synthase with maltokinase -

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Basic information

Entry
Database: PDB / ID: 5jy7
TitleComplex of Mycobacterium smegmatis trehalose synthase with maltokinase
Components
  • Maltokinase
  • Trehalose synthase/amylase TreS
KeywordsISOMERASE/TRANSFERASE / complex / isomerase / kinase / alpha glucan synthesis / isomerase-transferase complex
Function / homology
Function and homology information


maltokinase / trehalose metabolic process / maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / maltose metabolic process / trehalose biosynthetic process / carbohydrate phosphorylation / alpha-amylase / glycogen biosynthetic process / alpha-amylase activity ...maltokinase / trehalose metabolic process / maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / maltose metabolic process / trehalose biosynthetic process / carbohydrate phosphorylation / alpha-amylase / glycogen biosynthetic process / alpha-amylase activity / glycogen metabolic process / polysaccharide catabolic process / kinase activity / calcium ion binding / ATP binding
Similarity search - Function
Maltokinase N-terminal cap domain / Maltokinase N-terminal cap domain / Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Aminoglycoside phosphotransferase ...Maltokinase N-terminal cap domain / Maltokinase N-terminal cap domain / Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Protein kinase-like domain superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Maltokinase / Trehalose synthase/amylase TreS
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFutterer, K. / Kermani, A.A. / Besra, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K012118/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of the TreS-Pep2 complex, initiating alpha-glucan synthesis in the GlgE pathway of mycobacteria.
Authors: Kermani, A.A. / Roy, R. / Gopalasingam, C. / Kocurek, K.I. / Patel, T.R. / Alderwick, L.J. / Besra, G.S. / Futterer, K.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trehalose synthase/amylase TreS
B: Trehalose synthase/amylase TreS
C: Trehalose synthase/amylase TreS
D: Trehalose synthase/amylase TreS
E: Trehalose synthase/amylase TreS
F: Trehalose synthase/amylase TreS
G: Trehalose synthase/amylase TreS
H: Trehalose synthase/amylase TreS
I: Maltokinase
J: Maltokinase
K: Maltokinase
L: Maltokinase
M: Maltokinase
N: Maltokinase
O: Maltokinase
P: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)937,30724
Polymers936,98616
Non-polymers3218
Water00
1
A: Trehalose synthase/amylase TreS
B: Trehalose synthase/amylase TreS
C: Trehalose synthase/amylase TreS
D: Trehalose synthase/amylase TreS
I: Maltokinase
J: Maltokinase
K: Maltokinase
L: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,65412
Polymers468,4938
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Trehalose synthase/amylase TreS
F: Trehalose synthase/amylase TreS
G: Trehalose synthase/amylase TreS
H: Trehalose synthase/amylase TreS
M: Maltokinase
N: Maltokinase
O: Maltokinase
P: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,65412
Polymers468,4938
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)315.680, 315.680, 124.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASPAA13 - 58613 - 586
21HISHISPROPROBB17 - 58717 - 587
31HISHISASPASPCC9 - 5869 - 586
41HISHISPROPRODD17 - 58717 - 587
51LEULEUASPASPEE29 - 58629 - 586
61HISHISPROPROFF17 - 58717 - 587
71HISHISPROPROGG17 - 58717 - 587
81LEULEUASPASPHH29 - 58629 - 586
12SERSERLEULEUII2 - 4392 - 439
22SERSERTYRTYRJJ2 - 4092 - 409
32ASPASPLEULEUKK84 - 43984 - 439
42METMETLEULEULL1 - 4391 - 439
52SERSERLEULEUMM2 - 4392 - 439
62ASPASPLEULEUNN88 - 43988 - 439
72ALAALALEULEUOO198 - 439198 - 439
82ALAALALEULEUPP198 - 439198 - 439

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.153821, 0.690912, 0.706385), (0.670048, -0.452477, 0.588474), (0.726206, 0.563831, -0.393344)-48.36491, 97.623222, -35.301231
3given(-0.283169, -0.956545, 0.069547), (-0.956451, 0.276296, -0.094141), (0.070834, -0.093176, -0.993127)89.932007, 70.034843, 31.80864
4given(-0.571224, 0.282359, -0.770699), (0.274676, -0.81907, -0.503664), (-0.77347, -0.499397, 0.390316)7.54452, 145.292679, 56.49519
5given(-0.339632, 0.798273, -0.497403), (-0.888223, -0.446161, -0.109546), (-0.309369, 0.4046, 0.860575)-132.469055, 84.262497, -87.178093
6given(-0.789944, 0.025606, 0.612645), (0.155604, 0.974793, 0.159894), (-0.593107, 0.221638, -0.774016)-55.502201, -73.736458, -55.371971
7given(0.203081, -0.926431, -0.316992), (0.768063, 0.351516, -0.535271), (0.607319, -0.134767, 0.782944)189.308334, 84.994087, 72.174782
8given(0.957281, 0.161804, 0.239651), (0.009961, -0.846746, 0.531904), (0.288988, -0.506795, -0.812185)59.784351, 208.83168, 131.55043
9given(1), (1), (1)
10given(-0.22636, 0.638542, 0.735544), (0.690924, -0.427019, 0.583334), (0.686575, 0.640249, -0.344524)-45.465611, 96.018341, -40.045658
11given(-0.296219, -0.946164, 0.130493), (-0.954972, 0.290989, -0.057914), (0.016825, -0.141772, -0.989756)88.092102, 67.689697, 39.14035
12given(-0.514718, 0.29968, -0.803279), (0.317527, -0.803666, -0.503286), (-0.796393, -0.514113, 0.318505)5.1303, 143.249924, 62.317501
13given(-0.72317, -0.095502, 0.684036), (0.03415, 0.984238, 0.173519), (-0.689826, 0.148844, -0.70851)-36.264969, -79.49147, -49.43568
14given(-0.207132, 0.767954, -0.606089), (-0.946547, -0.313903, -0.074251), (-0.247274, 0.558312, 0.791924)-120.802673, 63.40432, -105.168823
15given(0.026532, -0.937793, -0.346179), (0.830072, 0.213633, -0.515112), (0.557024, -0.273687, 0.784104)172.958786, 117.67025, 92.958168
16given(0.905387, 0.307178, 0.293115), (0.127848, -0.855547, 0.501692), (0.404882, -0.416752, -0.813873)25.927429, 225.805374, 127.887917

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Components

#1: Protein
Trehalose synthase/amylase TreS / Maltose alpha-D-glucosyltransferase / MTase


Mass: 68272.133 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: treS, MSMEG_6515, MSMEI_6343 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R6E0, alpha-amylase, maltose alpha-D-glucosyltransferase
#2: Protein
Maltokinase / MaK / Maltose-1-phosphate synthase


Mass: 48851.172 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: mak, pep2, MSMEG_6514, MSMEI_6342 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R6D9, maltokinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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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: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 9% v/v polyethylene glycol 8000, 4% v/v glycerol, 200 mM MgCl2 and 0.1 M Tris HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 3.6→49.91 Å / Num. obs: 142362 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 126 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 9.1
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 7 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZO9

3zo9


Resolution: 3.6→49.9 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.88 / SU B: 92.904 / SU ML: 0.621 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.665
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 7119 5 %RANDOM
Rwork0.2612 ---
obs0.2622 135356 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 331.28 Å2 / Biso mean: 111.4 Å2 / Biso min: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 3.6→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56335 0 8 0 56343
Biso mean--20.01 --
Num. residues----7428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01957908
X-RAY DIFFRACTIONr_bond_other_d0.0020.0250599
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.94279206
X-RAY DIFFRACTIONr_angle_other_deg0.823115528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5657396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48623.2692808
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.152157658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.915457
X-RAY DIFFRACTIONr_chiral_restr0.0530.28467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02168246
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0214151
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 538 -
Rwork0.329 9818 -
all-10356 -
obs--98.96 %
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)
12.42990.2410.07591.06030.03171.31730.04330.45480.0269-0.3733-0.0522-0.3882-0.04880.34340.00890.45650.0740.16330.3170.06250.150718.17765.982-18.808
20.98360.0678-0.1991.21490.65282.32370.0178-0.16080.06990.0787-0.04940.1886-0.1408-0.4450.03160.220.07860.03440.20150.01150.0384-19.77969.57121.323
31.26470.3293-0.22861.3869-0.46781.5393-0.0904-0.28530.24840.37240.019-0.311-0.05160.16240.07140.39770.0472-0.11170.2446-0.08250.158820.6772.37345.654
40.85910.04380.3831.3827-0.30812.7393-0.15760.24380.5656-0.154-0.0362-0.577-0.65590.46510.19390.5753-0.22290.02370.31380.20740.781430.477105.9132.95
52.6522-1.40820.43993.0933-1.05292.39170.72851.0536-0.0881-1.0576-0.7289-0.3998-0.0481-0.00370.00041.1330.53650.07081.0060.03450.437-56.034155.477-13.781
65.3329-2.8065-1.08273.69470.5962.3256-0.8411-1.7457-0.36081.80580.7044-0.09340.40990.09340.13671.59970.1432-0.181.15860.20230.4524-57.877145.6338.935
72.7236-1.3258-0.32452.4060.51641.7850.7461.3995-0.6867-0.7592-0.77231.20820.0995-0.8190.02621.13270.4772-0.40281.7905-0.42171.1132-105.121164.307-6.523
85.047-2.0062-0.3413.9632.33495.1311-0.1578-0.97711.42760.73420.1606-0.4517-1.085-0.1341-0.00281.55040.0237-0.0671.0897-0.38141.2313-85.526190.23435.822
93.25621.09891.98741.1770.0312.7501-0.14980.5485-0.544-0.32870.2037-0.40940.5750.2467-0.05390.4029-0.05450.13970.2728-0.01460.3898-22.91127.905-1.553
101.71350.98580.92374.94661.27283.1696-0.098-0.02040.2260.11690.00790.8333-0.0218-1.28050.09010.76070.1760.0390.93130.10230.1542-25.46167.501-37.543
114.24530.98831.1343.12581.65293.2965-0.1734-0.4611-0.29320.60690.1882-0.70550.23751.853-0.01480.7673-0.1171-0.07671.85540.16481.746769.61696.06823.776
124.22351.88431.90261.85081.17851.6178-0.14250.07440.75130.12880.02410.0313-0.69180.12940.11841.36750.1453-0.38710.6846-0.37281.075128.491117.4660.006
133.2041-3.45910.60444.3350.01041.41510.69660.3324-0.3785-0.9665-0.94680.70620.4792-0.18240.25021.42590.4699-0.13770.9546-0.16130.997-39.202111.534-6.122
144.777-1.65640.86123.62770.78510.70940.19730.07470.46110.46350.1825-2.0740.15230.5334-0.37971.1905-0.0472-0.8521.3090.09442.5717-13.744149.18327.753
156.0877-0.5214-2.4080.5876-0.10051.2576-0.5907-1.0915-1.52470.28970.39611.0019-0.0088-0.27470.19462.20090.46820.99242.53850.35211.9872-128.819176.98543.564
161.9133-1.2171.40563.3286-1.08112.23120.18510.44031.2019-0.2629-0.63330.1902-1.1110.11180.44822.00490.92920.25082.17090.57422.0992-108.366209.919-12.384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 586
2X-RAY DIFFRACTION2B17 - 587
3X-RAY DIFFRACTION3C9 - 586
4X-RAY DIFFRACTION4D17 - 587
5X-RAY DIFFRACTION5E29 - 586
6X-RAY DIFFRACTION6F17 - 587
7X-RAY DIFFRACTION7G17 - 587
8X-RAY DIFFRACTION8H29 - 586
9X-RAY DIFFRACTION9I2 - 439
10X-RAY DIFFRACTION10J2 - 439
11X-RAY DIFFRACTION11K84 - 439
12X-RAY DIFFRACTION12L1 - 439
13X-RAY DIFFRACTION13M2 - 439
14X-RAY DIFFRACTION14N88 - 439
15X-RAY DIFFRACTION15O198 - 439
16X-RAY DIFFRACTION16P198 - 439

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