[English] 日本語
Yorodumi
- PDB-8eyn: Crystal Structure of Human Mitochondrial NADP+ Malic Enzyme 3 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eyn
TitleCrystal Structure of Human Mitochondrial NADP+ Malic Enzyme 3 in Apo Form
ComponentsNADP-dependent malic enzyme, mitochondrial
KeywordsOXIDOREDUCTASE / Malic Enzyme / Rossmann fold / ME3 / NADP(+)-binding
Function / homology
Function and homology information


oxygen metabolic process / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NADP+ binding / aerobic respiration ...oxygen metabolic process / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NADP+ binding / aerobic respiration / NAD binding / mitochondrial matrix / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain ...Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRIC ACID / NADP-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsShaffer, P.L. / Grell, T.A.J. / Mason, M. / Thompson, A.A. / Riley, D. / Wagner, M.V. / Steele, R. / Ortiz-Meoz, R. / Wadia, J. / Sharma, S. / Yu, X.
CitationJournal: Heliyon / Year: 2022
Title: Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer.
Authors: Tsehai A J Grell / Mark Mason / Aaron A Thompson / Jose Carlos Gómez-Tamayo / Daniel Riley / Michelle V Wagner / Ruth Steele / Rodrigo F Ortiz-Meoz / Jay Wadia / Paul L Shaffer / Gary ...Authors: Tsehai A J Grell / Mark Mason / Aaron A Thompson / Jose Carlos Gómez-Tamayo / Daniel Riley / Michelle V Wagner / Ruth Steele / Rodrigo F Ortiz-Meoz / Jay Wadia / Paul L Shaffer / Gary Tresadern / Sujata Sharma / Xiaodi Yu /
Abstract: Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent ...Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP-dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
History
DepositionOct 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADP-dependent malic enzyme, mitochondrial
B: NADP-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0434
Polymers127,6592
Non-polymers3842
Water19,7981099
1
A: NADP-dependent malic enzyme, mitochondrial
B: NADP-dependent malic enzyme, mitochondrial
hetero molecules

A: NADP-dependent malic enzyme, mitochondrial
B: NADP-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,0868
Polymers255,3174
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area18090 Å2
ΔGint-87 kcal/mol
Surface area81990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.750, 75.130, 118.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1092-

HOH

-
Components

#1: Protein NADP-dependent malic enzyme, mitochondrial / NADP-ME / Malic enzyme 3


Mass: 63829.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16798, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1099 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.1M Ammonium Tartrate dibasic, 12% PEG-3350, 0.02 Potassium Citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→38.5 Å / Num. obs: 100206 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.45 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.12 / Rsym value: 0.11 / Net I/σ(I): 13.37
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 49564 / CC1/2: 0.698 / Rrim(I) all: 1.09 / Rsym value: 1.01 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS20180409data reduction
XSCALE20180409data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR6

1qr6


Resolution: 1.94→38.5 Å / SU ML: 0.1799 / Cross valid method: FREE R-VALUE / Phase error: 18.736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 2217 2.21 %
Rwork0.1631 97961 -
obs0.1636 100178 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.38 Å2
Refinement stepCycle: LAST / Resolution: 1.94→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8770 0 26 1099 9895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00379105
X-RAY DIFFRACTIONf_angle_d0.610612399
X-RAY DIFFRACTIONf_chiral_restr0.04371405
X-RAY DIFFRACTIONf_plane_restr0.00381608
X-RAY DIFFRACTIONf_dihedral_angle_d2.44717469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.28821370.24426024X-RAY DIFFRACTION98.65
1.98-2.030.261360.22476024X-RAY DIFFRACTION99.07
2.03-2.080.25671360.22696007X-RAY DIFFRACTION99.18
2.08-2.140.25091370.19576094X-RAY DIFFRACTION99.46
2.14-2.20.20141390.18676101X-RAY DIFFRACTION99.43
2.2-2.270.26621360.225977X-RAY DIFFRACTION98.52
2.27-2.350.19271380.17276085X-RAY DIFFRACTION99.28
2.35-2.450.19731370.17076067X-RAY DIFFRACTION99.6
2.45-2.560.20721370.17446104X-RAY DIFFRACTION99.63
2.56-2.690.22781400.17586111X-RAY DIFFRACTION99.49
2.69-2.860.21371380.16866127X-RAY DIFFRACTION99.51
2.86-3.080.18281380.16926131X-RAY DIFFRACTION99.7
3.08-3.390.18891410.1546187X-RAY DIFFRACTION99.61
3.39-3.880.15951390.1366175X-RAY DIFFRACTION99.42
3.88-4.890.12291430.12166252X-RAY DIFFRACTION99.6
4.89-38.50.15811450.15586495X-RAY DIFFRACTION99.51
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)
10.340414787975-0.4002998732140.09400980834072.331506878850.2123613638330.122242808343-0.045628334214-0.0892531504237-0.07683566448330.2741808511220.0653095227330.02185156571310.03296129730490.0102686284388-0.01435029192180.2257354386380.0223859060309-0.002697394601270.1997883860470.01920061098840.24490342242666.83737.26836.183
21.31188714805-0.0532211112151-0.226006856160.455631843560.05153599327050.2903655697550.0218321552641-0.01287240183970.08612457823140.08025950771590.0132074540882-0.0448942388984-0.0316477755675-0.0141738940885-0.0389189096720.211627525074-9.52886359791E-50.007285763605540.158934637303-0.00562663891190.19157565774363.51160.37532.433
30.727210329733-0.209915828952-0.2949872691981.263881255620.674106921251.82459228536-0.0334875173755-0.140873630650.02611124445460.2379796864220.02100415554270.0562680624051-0.07447108816620.08551233458890.01706579329920.218669845513-0.01605115881420.01575247920870.2162131569540.01232060748610.19771706134644.47962.06145.122
42.541308203490.1051665365421.641809132382.87445482832.106000964997.88150005330.00557161740348-0.441752267172-0.1175196257480.7107778565160.289388276193-0.1765484165730.109930340732-0.0771531892884-0.1444396986690.364159676850.075121200044-0.02491753754240.3221181363920.07418345880990.4130017876855.91225.0669.757
53.687226786581.21167187007-2.817067815074.18670648996-1.700889894982.4691944675-0.005821955929440.179412909436-0.419802397210.179571295144-0.1046344239370.2188348550240.228945832346-0.1285131664920.05831008832940.260109317146-0.0343185579803-0.0158963923110.303710057339-0.008972073252350.4603565720253.88217.472-7.736
66.51178136391-2.16809337141-2.690493529232.248160499451.045663332122.06150697862-0.01872837896980.930218984816-0.862661650232-0.698563315574-0.0227736996229-0.03197996546560.6290352723870.0810819186240.0681886623750.35285819542-0.01272715945390.01114037931630.425570896855-0.09436180351210.4540296887262.51915.153-16.059
72.255945426920.3162660637710.1810414916470.55036412706-0.01363678611920.369886979476-0.02080428054940.2446318634540.0645099717479-0.06776122353840.021108739567-0.04878326767770.003653163225890.0278924734413-0.00376540961910.1790360184540.02868064609910.02343783584150.218925943228-0.006256333474630.22364059278973.42846.148-11.838
80.568444056739-0.2560081856670.1647785437681.38649746835-0.02776426409080.2760295928920.006296841901140.0352311432303-0.097914724718-0.0457688924514-0.007900775749120.053819723579-0.0060628217558-0.0473608628852-0.0035179547810.1420779496560.0006969131514810.006280001467810.213532102193-0.009323743677820.18327711687550.30542.779-7.954
92.127114733190.690214836631-0.09032608503912.39554920040.7457223147513.10420128729-0.06792193584070.05564890906160.0203156290736-0.182155000021-0.05006575942580.159742298527-0.0154461520413-0.2120552161880.1084443160720.1639952518580.0403953779287-0.04008346703130.226844910285-0.0247157172460.19916232643534.88357.612-27.401
101.063902288940.1593458061521.384810613450.2661160288890.2961141074922.14851590498-0.06279041138130.09593188312170.0578254078707-0.0614566492519-0.00254885698209-0.04445470106-0.205874719990.1318560022340.07085045378650.15957188643-0.003016584597030.01917251372970.1473522773350.01426478601780.21346809004359.17563.55-5.032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 49:164 )A49 - 164
2X-RAY DIFFRACTION2( CHAIN A AND RESID 165:323 )A165 - 323
3X-RAY DIFFRACTION3( CHAIN A AND RESID 324:584 )A324 - 584
4X-RAY DIFFRACTION4( CHAIN A AND RESID 585:595 )A585 - 595
5X-RAY DIFFRACTION5( CHAIN A AND RESID 596:602 )A596 - 602
6X-RAY DIFFRACTION6( CHAIN A AND RESID 603:610 )A603 - 610
7X-RAY DIFFRACTION7( CHAIN B AND RESID 49:164 )B49 - 164
8X-RAY DIFFRACTION8( CHAIN B AND RESID 165:323 )B165 - 323
9X-RAY DIFFRACTION9( CHAIN B AND RESID 324:463 )B324 - 463
10X-RAY DIFFRACTION10( CHAIN B AND RESID 464:610 )B464 - 610

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more