PDB-8hmq: Crystal Structure of PKM2 mutant P403A

ID or keywords:

Entry

Database: PDB / ID: 8hmq

Title

Crystal Structure of PKM2 mutant P403A

Components

Pyruvate kinase PKM

Keywords

TRANSFERASE /

PKM2 /

Hydroxylation /

Kinase /

Glycolysis / Tumour Promoting / Warburg Effect

Function / homology

Function and homology information

programmed cell death /

pyruvate kinase /

pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis /

Glycolysis / positive regulation of sprouting angiogenesis /

potassium ion binding /

rough endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Upadhyay, S. / Kumar, A. / Patel, A.K.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2
Authors: Upadhyay, S. / Kumar, A. / Patel, A.K.

History

Deposition	Dec 5, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 11, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8hmq.cif.gz	887.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8hmq.ent.gz	614.2 KB	Display	PDB format
PDBx/mmJSON format	8hmq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/8hmq ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hmq	HTTPS FTP

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Related structure data

Related structure data	8hmrC 8hmsC 8hmuC 3gr4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (15) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Pyruvate kinase PKM

B: Pyruvate kinase PKM

C: Pyruvate kinase PKM

D: Pyruvate kinase PKM

hetero molecules

243 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	99.829, 136.839, 149.160
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 13 or (resid 14 and (name...
d_2	ens_1	(chain "B" and (resid 13 through 55 or (resid 56...
d_3	ens_1	(chain "C" and (resid 13 or (resid 14 and (name...
d_4	ens_1	(chain "D" and (resid 13 or (resid 14 and (name...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	ILE	THR	A	1 - 109
d_1	2	ens_1	GLU	LYS	A	111 - 115
d_1	3	ens_1	THR	ILE	A	119 - 122
d_1	4	ens_1	ASP	ASP	A	124
d_1	5	ens_1	GLU	GLU	A	133
d_1	6	ens_1	ILE	ILE	A	138
d_1	7	ens_1	ASP	ASP	A	142
d_1	8	ens_1	GLY	GLY	A	156
d_1	9	ens_1	LYS	PRO	A	159 - 164
d_1	10	ens_1	ASP	PRO	A	169 - 469
d_1	11	ens_1	PHE	PRO	A	471 - 481
d_1	12	ens_1	OXL	OXL	B
d_2	1	ens_1	ILE	THR	H	1 - 109
d_2	2	ens_1	GLU	LYS	H	116 - 120
d_2	3	ens_1	THR	ILE	H	124 - 127
d_2	4	ens_1	ASP	ASP	H	145
d_2	5	ens_1	GLU	ILE	H	154 - 155
d_2	6	ens_1	ASP	ASP	H	159
d_2	7	ens_1	GLY	GLY	H	178
d_2	8	ens_1	LYS	PRO	H	185 - 190
d_2	9	ens_1	ASP	PRO	H	195 - 495
d_2	10	ens_1	PHE	PRO	H	499 - 509
d_2	11	ens_1	OXL	OXL	I
d_3	1	ens_1	ILE	THR	M	1 - 109
d_3	2	ens_1	GLU	LYS	M	114 - 118
d_3	3	ens_1	THR	LEU	M	122 - 123
d_3	4	ens_1	LYS	LYS	M	130
d_3	5	ens_1	ILE	ILE	M	135
d_3	6	ens_1	ASP	ASP	M	139
d_3	7	ens_1	GLU	GLU	M	145
d_3	8	ens_1	ILE	ILE	M	150
d_3	9	ens_1	ASP	ASP	M	154
d_3	10	ens_1	GLY	GLY	M	163
d_3	11	ens_1	LYS	PRO	M	166 - 483
d_3	12	ens_1	OXL	OXL	N
d_4	1	ens_1	ILE	THR	Q	1 - 109
d_4	2	ens_1	GLU	LYS	Q	119 - 123
d_4	3	ens_1	THR	ILE	Q	127 - 130
d_4	4	ens_1	ASP	ASP	Q	133
d_4	5	ens_1	GLU	GLU	Q	142
d_4	6	ens_1	ILE	ILE	Q	144
d_4	7	ens_1	ASP	ASP	Q	148
d_4	8	ens_1	GLY	GLY	Q	158
d_4	9	ens_1	LYS	PRO	Q	165 - 170
d_4	10	ens_1	ASP	PRO	Q	175 - 475
d_4	11	ens_1	PHE	PRO	Q	479 - 489
d_4	12	ens_1	OXL	OXL	R

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.0774647257689, 0.190166588237, 0.978690903697), (0.17988740703, -0.968195818038, 0.17388898391), (0.980632314914, 0.162583906497, -0.109209597996)	22.7209104001, -1.52126807933, -25.2664526469
2	given	(-0.667059847862, 0.555029472159, -0.496964228497), (0.615980571712, 0.0356894126078, -0.786952477029), (-0.419045456537, -0.831064709191, -0.365694345722)	-8.26378759525, -19.5201118582, -32.5426032648
3	given	(-0.358154117403, -0.732163950649, -0.579363079215), (-0.8025345658, -0.0757020772091, 0.591783293277), (-0.477141382489, 0.676908520316, -0.56047386758)	-13.3629614875, 10.3628100901, -32.8694953849

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein

Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...

Mass: 60162.211 Da / Num. of mol.: 4 / Mutation: P403A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host:

Escherichia coli (E. coli)
References: UniProt: P14618,

pyruvate kinase,

non-specific serine/threonine protein kinase,

non-specific protein-tyrosine kinase

#6: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose /

Fructose 1,6-bisphosphate

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 135 molecules

#2: Chemical	ChemComp-OXL / OXALATE ION / Oxalate Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂O₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP buffer, pH 7.0, 25 % w/v PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97989 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97989 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.33 Å / Num. obs: 71344 / % possible obs: 100 % / Redundancy: 8.2 % / B_iso Wilson estimate: 48.53 Å² / CC_1/2: 0.99 / Net I/σ(I): 17.3
Reflection shell	Resolution: 2.5→2.56 Å / Num. unique obs: 4528 / CC_1/2: 0.82

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	1.20.1_4487	data reduction
Aimless		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GR4

3gr4

Resolution: 2.5→46.73 Å / SU ML: 0.3472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2627	3557	5 %
R_work	0.2135	67648	-
obs	0.2159	71205	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 60.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→46.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14635	0	127	110	14872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	14963
X-RAY DIFFRACTION	f_angle_d	0.6581	20264
X-RAY DIFFRACTION	f_chiral_restr	0.0473	2377
X-RAY DIFFRACTION	f_plane_restr	0.0056	2637
X-RAY DIFFRACTION	f_dihedral_angle_d	6.3051	2116

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	1.0211665413
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	2.09742203607
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	2.41037593097

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.53	0.3929	136	0.2889	2681	X-RAY DIFFRACTION	99.96
2.53-2.57	0.3821	137	0.2695	2676	X-RAY DIFFRACTION	99.96
2.57-2.61	0.339	145	0.2703	2644	X-RAY DIFFRACTION	99.89
2.61-2.65	0.3197	145	0.2559	2672	X-RAY DIFFRACTION	100
2.65-2.69	0.3475	128	0.2534	2695	X-RAY DIFFRACTION	100
2.69-2.74	0.2839	139	0.2413	2678	X-RAY DIFFRACTION	100
2.74-2.79	0.3056	148	0.2423	2665	X-RAY DIFFRACTION	99.93
2.79-2.84	0.2748	151	0.2519	2679	X-RAY DIFFRACTION	99.93
2.84-2.9	0.3237	135	0.2509	2675	X-RAY DIFFRACTION	99.96
2.9-2.96	0.286	140	0.255	2706	X-RAY DIFFRACTION	99.96
2.96-3.03	0.3755	120	0.2564	2712	X-RAY DIFFRACTION	99.82
3.03-3.11	0.2714	144	0.2357	2674	X-RAY DIFFRACTION	99.89
3.11-3.19	0.2885	130	0.229	2691	X-RAY DIFFRACTION	99.86
3.19-3.29	0.27	120	0.2222	2695	X-RAY DIFFRACTION	99.96
3.29-3.39	0.2631	139	0.2268	2710	X-RAY DIFFRACTION	99.96
3.39-3.51	0.2982	171	0.221	2675	X-RAY DIFFRACTION	99.82
3.51-3.65	0.26	131	0.217	2697	X-RAY DIFFRACTION	99.79
3.65-3.82	0.2651	163	0.1993	2712	X-RAY DIFFRACTION	99.86
3.82-4.02	0.2623	144	0.194	2699	X-RAY DIFFRACTION	99.61
4.02-4.27	0.2344	142	0.1898	2712	X-RAY DIFFRACTION	99.79
4.27-4.6	0.2114	125	0.175	2746	X-RAY DIFFRACTION	99.76
4.6-5.07	0.2246	163	0.1773	2715	X-RAY DIFFRACTION	99.97
5.07-5.8	0.2302	150	0.2187	2762	X-RAY DIFFRACTION	99.93
5.8-7.3	0.2547	168	0.2224	2768	X-RAY DIFFRACTION	100
7.31-46.73	0.2284	143	0.1911	2909	X-RAY DIFFRACTION	99.48

Refinement TLS params.

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

ID	L11 (°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)
1	2.00303395512	-1.17633011137	0.565564425047	2.13662973169	-0.670056274516	0.989417537588	-0.0822281539703	-0.2635101207	0.118910785174	0.00447357247732	0.0217668796768	0.161900393425	0.0231199481858	-0.246099152387	0.0864480574331	0.381432744238	0.00211787444241	0.00548508152799	0.352933728016	-0.0895180970588	0.438356867579	-31.0002034651	5.30492669426	-33.2775531671
2	2.01151573262	-2.07033049691	-0.999053415209	3.00642092144	2.35175317713	5.38743145589	0.231995544085	0.473681138155	-0.282494772574	-0.959371662844	-0.564064557688	0.334113207553	-0.400863870413	0.140601348039	0.331936103403	0.755528789371	0.0255903924622	-0.17849797229	0.476068605886	-0.0553024941358	0.602234427681	-23.6694507684	9.17561727937	-59.2004488498
3	1.71595300925	-0.202181621328	-0.450664528585	1.96682756691	-0.169045945315	1.41924843931	0.0249260500985	0.18290464013	0.229778998985	-0.235018837723	-0.115417303422	0.0268036210283	-0.195747883527	0.00988451053806	0.0961484049648	0.37043136456	-0.00184163954251	-0.0419534464281	0.278999912468	-0.0258800854816	0.303846678347	-21.7719263314	9.9775641825	-44.0838822522
4	2.368953694	-0.358277160528	0.723971119893	1.93626405992	0.333497394702	2.50902597823	-0.0767371611138	-0.168901542394	0.0184366026892	0.290890291075	-0.0205341092551	0.105428661014	-0.155531077881	0.108567665018	0.0805714177585	0.439278947585	0.0118816072219	0.00974518707387	0.360266515378	-0.0443659255771	0.340822907091	-21.7796112285	15.0020213167	-17.8782090201
5	0.75258629653	-0.45766146415	0.170477301436	2.37268498759	0.801248867778	1.41696187277	0.120643604578	0.207248003006	-0.112182609343	-0.454623699498	0.00350666373153	-0.0045746329798	0.0576372776811	0.0985402787968	-0.132025376478	0.436035319585	0.056746696886	0.0085350880397	0.378116118639	-0.072364784828	0.394189554516	-11.6266468824	-18.2298334997	-50.7508798288
6	4.21960488106	-0.0547588238483	-0.484243479409	1.38593653159	0.318827541351	1.526778637	0.169199707662	-0.0433566595684	-0.0224404837797	0.093255321058	-0.231265901778	0.479340714569	0.127613524602	-0.872279911942	0.142924162734	0.664181674747	-0.0439542428299	-0.000598471453279	0.717014454545	-0.16584330415	0.707000921996	-38.1392740826	-26.8088138166	-41.5689075109
7	1.39316024708	-0.425091738954	0.110731460498	1.23974610307	0.29237707483	0.887172943958	0.0553598098942	-0.0095810839933	-0.273674295274	-0.0577395505905	-0.0221556483435	0.00726464664445	0.167363193896	0.100326001373	-0.025665285978	0.380546092193	0.050132605442	0.0247685315495	0.242448509924	-0.0121708022361	0.376278653652	-7.06799393377	-22.8853340955	-41.1767339283
8	3.73920426928	-0.00878610447347	-0.730635334965	1.71320321451	0.206974367953	1.67914986084	-0.241682166049	0.0869609189989	-0.533142269546	-0.0404940360387	0.0902777679231	-0.402514864981	0.105450381477	0.633217349941	0.12991358307	0.361523400305	0.065226907549	0.00268455354215	0.742323548195	0.0938083077778	0.418374804982	34.4250757247	-9.60987995072	-12.4388886528
9	1.92571717269	0.895706887361	0.504355060128	1.91500618835	1.71300843975	2.16145867277	0.0900715007156	-0.401718659244	1.04662674044	0.19031036682	0.391042145765	-0.227175051279	0.407878316483	0.515718064787	-0.515323173439	0.716135110401	-0.117782391102	0.128744950415	0.919426331732	-0.208214551593	1.08942693862	46.1111824587	17.8240555311	-5.71101879543
10	1.49387030524	0.0360496784365	-0.494736297281	1.08685808532	0.594678878281	1.93409666455	0.00837805639079	0.0373804345475	-0.101236792334	-0.136783838436	-0.0692882277571	-0.231649690732	-0.241358492944	0.625343997162	0.059296096794	0.346824710427	-0.0044910532204	0.0414238202816	0.651403474375	0.146545235568	0.498479643501	28.9005377579	-3.16786357402	-20.0807225725
11	2.03535538217	0.411237204632	0.198294067546	1.63808573574	0.0777518192634	1.31463202201	-0.109923054505	0.162815048996	-0.528402508828	-0.0748754035473	-0.0124933982978	-0.296579220365	0.623379074858	0.745433705712	0.131249036591	0.544244213835	0.205168049906	0.196357043418	0.787125206597	0.0125846127669	0.74176106193	27.0804729889	-25.4030649551	-29.8156262406
12	0.884887470793	-0.290656865035	-0.253444264654	2.51079157952	1.97576550076	3.10679983427	0.00188319483482	-0.32017990096	0.0526074263182	0.125209878896	-0.11182856844	-0.146627216394	-0.431302139631	0.0904417510244	0.109738348246	0.3906342361	-0.108567157586	-0.0303033328197	0.607622763454	0.0722523654638	0.435849537205	12.8090678944	13.3803719962	6.73523995356
13	2.95617019201	-0.108048146822	0.0761501079865	0.32381797515	-0.894270007953	2.40994719035	-0.52193249586	-0.265298599178	0.432114371851	0.215667903645	-0.122567250806	-0.373489358295	-0.231509207922	0.466892757457	0.311578081134	0.89692565869	0.162580528005	0.0132861570021	0.968255273487	0.230641197865	0.850516790294	28.5428781745	-7.55307121033	23.2573430856
14	1.39356048175	-0.460814670995	-0.258239613412	0.923585693107	-0.133121074283	1.13356655808	-0.0852132597861	-0.281404337567	-0.0871291413219	0.136469060387	-0.0785115653425	0.0181825866746	-0.168880235226	0.0344151306949	0.174383264676	0.421609742147	-0.0279236382534	-0.0248430872219	0.502219254475	0.0365473326212	0.337680635643	4.78865910138	6.71563096916	4.091307102
15	6.61703043991	3.52761081524	1.51778641871	7.51577926154	0.0145364956272	1.30869024476	0.464857771778	-0.135066626355	0.0121794770471	0.73126100463	-0.334359742355	0.231309129064	-0.653222661076	-0.0738955196662	-0.173023481363	0.618986515585	0.0185985876627	-0.0381478244728	0.455790750391	-0.0389182337091	0.356796335975	-8.86741739202	22.2176890707	-4.19277657088

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 13 through 98 )	A	A	13 - 98	1 - 86
2	2	chain 'A' and (resid 99 through 199 )	A	A	99 - 199	87 - 155
3	3	chain 'A' and (resid 200 through 388 )	A	A	200 - 388	156 - 340
4	4	chain 'A' and (resid 389 through 531 )	A	A	389 - 531	341 - 481
5	5	chain 'B' and (resid 13 through 98 )	B	H	13 - 98	1 - 86
6	6	chain 'B' and (resid 99 through 222 )	B	H	99 - 222	87 - 200
7	7	chain 'B' and (resid 223 through 531 )	B	H	223 - 531	201 - 509
8	8	chain 'C' and (resid 13 through 131 )	C	M	13 - 131	1 - 114
9	9	chain 'C' and (resid 132 through 222 )	C	M	132 - 222	115 - 177
10	10	chain 'C' and (resid 223 through 465 )	C	M	223 - 465	178 - 420
11	11	chain 'C' and (resid 466 through 531 )	C	M	466 - 531	421 - 483
12	12	chain 'D' and (resid 13 through 123 )	D	Q	13 - 123	1 - 111
13	13	chain 'D' and (resid 124 through 222 )	D	Q	124 - 222	112 - 180
14	14	chain 'D' and (resid 223 through 499 )	D	Q	223 - 499	181 - 457
15	15	chain 'D' and (resid 500 through 531 )	D	Q	500 - 531	458 - 489

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