Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass

Nowicki, M.W.; Kuaprasert, B.; McNae, I.W.; Morgan, H.P.; Harding, M.M.; Michels, P.A.; Fothergill-Gilmore, L.A.; Walkinshaw, M.D.; J. Mol. Biol. 394, 535-543 (2009)

 show all sequences of 5.4.2.1

Data extracted from this reference:

Cloned(Commentary)
Commentary Organism
His-tagged enzyme is expressed in Escherichia coli BL21 cells Leishmania mexicana
Crystallization (Commentary)
Crystallization Organism
iPGAM crystallized with 3-phosphoglycerate or 2-phosphoglycerate at high and low cobalt concentrations (4 mM and 0.01 mM), hanging drop vapor diffusion method, using 0.08 M ammonium acetate, 0.04 M trisodium citrate dihydrate pH 6.0, and 24% (w/v) PEG 4000 Leishmania mexicana
Metals/Ions
Metals/Ions Commentary Organism Structure
Co2+ two Co2+ are coordinated within the active site Leishmania mexicana
Organism
Organism Primary Accession No. (UniProt) Commentary Textmining
Leishmania mexicana Q86N96
-
-
Purification (Commentary)
Commentary Organism
metal affinity Talon column chromatography Leishmania mexicana
Substrates and Products (Substrate)
Substrates Commentary Substrates Literature (Substrates) Organism Products Commentary (Products) Literature (Products) Organism (Products) Reversibility
2-phospho-D-glycerate
-
 705169 Leishmania mexicana 3-phospho-D-glycerate
-
-
-
 r
Cofactor
Cofactor Commentary Organism Structure
additional information phosphoglycerate mutase is cofactor-independent Leishmania mexicana
-
Cloned(Commentary) (protein specific)
Commentary Organism
His-tagged enzyme is expressed in Escherichia coli BL21 cells Leishmania mexicana
Cofactor (protein specific)
Cofactor Commentary Organism Structure
additional information phosphoglycerate mutase is cofactor-independent Leishmania mexicana
-
Crystallization (Commentary) (protein specific)
Crystallization Organism
iPGAM crystallized with 3-phosphoglycerate or 2-phosphoglycerate at high and low cobalt concentrations (4 mM and 0.01 mM), hanging drop vapor diffusion method, using 0.08 M ammonium acetate, 0.04 M trisodium citrate dihydrate pH 6.0, and 24% (w/v) PEG 4000 Leishmania mexicana
Metals/Ions (protein specific)
Metals/Ions Commentary Organism Structure
Co2+ two Co2+ are coordinated within the active site Leishmania mexicana
Purification (Commentary) (protein specific)
Commentary Organism
metal affinity Talon column chromatography Leishmania mexicana
Substrates and Products (Substrate) (protein specific)
Substrates Commentary Substrates Literature (Substrates) Organism Products Commentary (Products) Literature (Products) Organism (Products) Reversibility
2-phospho-D-glycerate
-
 705169 Leishmania mexicana 3-phospho-D-glycerate
-
-
-
 r

See also following references to EC number 5.4.2.1 (sorted by year of publication):
No.1st authorPub
Med		titleorganimsjournalvolumepagesyearActivating CompoundApplicationCloned(Commentary)Crystallization (Commentary)EngineeringGeneral StabilityInhibitorsKM Value [mM]LocalizationMetals/IonsMolecular Weight [Da]Natural Substrates/ Products (Substrates)Organic Solvent StabilityOrganismOxidation StabilityPosttranslational ModificationPurification (Commentary)ReactionRenatured (Commentary)Source TissueSpecific Activity [micromol/min/mg]Storage StabilitySubstrates and Products (Substrate)SubunitsTemperature Optimum [°C]Temperature Range [°C]Temperature Stability [°C]Turnover Number [1/s]pH OptimumpH RangepH StabilityCofactorKi Value [mM]pI ValueIC50 ValueActivating Compound (protein specific)Application (protein specific)Cloned(Commentary) (protein specific)Cofactor (protein specific)Crystallization (Commentary) (protein specific)Engineering (protein specific)General Stability (protein specific)IC50 Value (protein specific)Inhibitors (protein specific)Ki Value [mM] (protein specific)KM Value [mM] (protein specific)Localization (protein specific)Metals/Ions (protein specific)Molecular Weight [Da] (protein specific)Natural Substrates/ Products (Substrates) (protein specific)Organic Solvent Stability (protein specific)Oxidation Stability (protein specific)Posttranslational Modification (protein specific)Purification (Commentary) (protein specific)Renatured (Commentary) (protein specific)Source Tissue (protein specific)Specific Activity [micromol/min/mg] (protein specific)Storage Stability (protein specific)Substrates and Products (Substrate) (protein specific)Subunits (protein specific)Temperature Optimum [°C] (protein specific)Temperature Range [°C] (protein specific)Temperature Stability [°C] (protein specific)Turnover Number [1/s] (protein specific)pH Optimum (protein specific)pH Range (protein specific)pH Stability (protein specific)pI Value (protein specific)ExpressionGeneral InformationGeneral Information (protein specific)Expression (protein specific)KCat/KM [mM/s]KCat/KM [mM/s] (protein specific)
716984LiIdentification and characteriz ...Dirofilaria immitis, Wolbachia sp.Vet. Parasitol.176350-3562011--2----2-----6--2---2-42---2---2-2---22------2-------2--2-42---2---2----22
705270KimuraHigh prevalence of autoantibod ...Rattus norvegicusJ. Neuroimmunol.219105-1082010-1---------1-3-----4--1-------------1------------1-----4--1---------------
705672RenQuantitative proteomics identi ...Homo sapiensMol. Cancer9812010-1--------11-3-----3--1----------1--1-----------11-----3--1--------11111--
706661HakobyanMolecular dynamics study of in ...Homo sapiensProteins781691-17042010-------------3--------1-----------------------------------1---------------
715964SolemPhosphoglycerate mutase is a h ...Lactococcus lactis subsp. lactisJ. Mol. Microbiol. Biotechnol.18174-1802010------11--1--3--------11---1---1------1----1-1--1---------11---1-----11---
694538FosterThe Wolbachia endosymbiont of ...Wolbachia sp.Parasitol. Res.1041047-10522009-11-------2--8--1-----1--------1----111---------2----1----1---------------
703707KowalskiPhosphoglycerate mutase in mam ...Oryctolagus cuniculus, Rattus norvegicusFEBS Lett.5831841-18452009--------1----3-----3--2-----------------------1--------3--2---------------
703862iaoAn insertion of intracisternal ...Mus musculusGenes Genet. Syst.84327-3342009-----------1-4-----2--1--------------------------1-----2--1---------------
705169NowickiCrystal structures of Leishman ...Leishmania mexicanaJ. Mol. Biol.394535-5432009--11-----1---4--1-----1--------1-----111-------1-----1----1---------------
690732KajiwaraPeony root extract upregulates ...Mus musculusBiochem. Biophys. Res. Commun.371375-37920082---------2--3-----1--1----------1-2------------2------1--1--------1------
692403SaavedraGlycolysis in Ustilago maydis ...Ustilago maydisFEMS Yeast Res.81313-13232008-------------4--------1--------1------1-------------------1---------------
693442QiuAssignment and expression patt ...Sus scrofaJ. Genet. Genomics35257-2602008--1-----2-1--7-----3--1--------------2--------4-2------6--2---------------
694050JacobowitzImmunohistochemical localizati ...Rattus norvegicusMicrovasc. Res.7689-932008-1--------1--3-----1--1----------1--1-----------1------1--1--------1------
678734NukuiStructure and molecular mechan ...Bacillus anthracisBiophys. J.92977-9882007--11---------5--11-21-2--------------1-1-------------1-21-2---------------
679715JohnsenCharacterization of cofactor-d ...Archaeoglobus fulgidus, Thermoplasma acidophilumExtremophiles11647-65720072-2-1-14-22--6----1-2-42--3-12-----2-2--1--1-4-22-----1-2-42--3-12--------
681851EvansMechanistic and structural req ...Homo sapiensMol. Biosyst.3495-5062007---11-1------3-------------------------11--1------------------------------
682237DjikengCofactor-independent phosphogl ...Trypanosoma bruceiParasitol. Res.100887-8922007----1--------3-----2--------------------1--------------2------------------
677357LokanathPurification, crystallization ...Pyrococcus horikoshiiActa Crystallogr. Sect. F62788-7902006--11---------4--1------1-------------1-1-------------1-----1--------------
677393KleinmanCrystallization and initial cr ...Mus musculusActa Crystallogr. Sect. FF62218-2202006--11---------2-----1-----------------1-1---------------1------------------
680944HakobyanInvestigation of interaction b ...Saccharomyces cerevisiaeJ. Biomol. Struct. Dyn.23625-6332006-------------3---------1-----------------------------------1--------------
660610MullerThe 1.70 angstroms X-ray cryst ...Mycobacterium tuberculosisActa Crystallogr. Sect. D61309-3152005--11---------3--1--------------------1-1-------------1--------------------
660633WatkinsCloning, expression, purificat ...Mycobacterium tuberculosisActa Crystallogr. Sect. FF61753-7552005--11------1--2---------1-------------1-1--------1----------1--------------
660903WangCrystal structure of human B-t ...Homo sapiensBiochem. Biophys. Res. Commun.3311207-12152005-1-1---------4---------1------------1--1-------------------1--------------
661261de AtauriCharacterization of the first ...Homo sapiensBiochim. Biophys. Acta1740403-4102005-1--1--1-----5---1-3--3---1---------1---1----1---------3--3---1-----------
661689SaavedraGlycolysis in Entamoeba histol ...Entamoeba histolyticaFEBS J.2721767-17832005--1----4-----4-------12----42--1-----11------4-----------12----42---------
661847RepisoPhosphoglycerate mutase BB iso ...Homo sapiensHaematologica90257-2592005-1--1--------1----------------------1---1---------------------------------
661634GuerraCharacterization of the cofact ...Leishmania mexicanaEur. J. Biochem.2711798-18102004--1--14231---5----121-21---211-1-1---11--1-4-231------121-21---211-1------
661851Gonzalez-CincaEffects of thyroid hormone and ...Oryctolagus cuniculusHorm. Res.62191-1962004-1-----------2-----5----------------1------------------5------------------
662259ZhangCofactor-independent phosphogl ...Brugia malayi, Caenorhabditis elegansJ. Biol. Chem.27937185-371902004--2-1-2------7------4-42-------2-----22-1--2------------4-42--------------
649202PoonpermExpression, purification, crys ...Leishmania mexicanaActa Crystallogr. Sect. D591313-13162003--11-------1-4--1-----1--------1-----111---------1---1----1---------------
651716PottersPhosphoprotein with phosphogly ...Sulfolobus solfataricusJ. Bacteriol.1852112-21212003---------3-1-3-11-----11-----------------------3-1--11----11--------------
652915RigdenInsights into the catalytic me ...Geobacillus stearothermophilusJ. Mol. Biol.328909-9202003--111------1-2--1-----1--------1-----1111--------1---1----1---------------
651372van der OostMolecular characterization of ...Methanocaldococcus jannaschii, Pyrococcus furiosusFEMS Microbiol. Lett.212111-1202002--2---42-222-6--2-----22----2--2-----22----4-2-222---2----22----2---------
652877BondMechanistic implications for E ...Escherichia coliJ. Mol. Biol.3161071-108120021-11-------1-5--1-----11-----------1-1-1---------1---1----11--------------
652846UhrinovaSolution structure and dynamic ...Schizosaccharomyces pombeJ. Mol. Biol.306275-2902001--1-1------1-4--1--1--11-------------1--1--------1---1-1--11--------------
650970JedrzejasStructure and mechanism of act ...Geobacillus stearothermophilusEMBO J.191419-14312000--1112----1-1-3--1-----1-----11-1-----11112------1-1---1----1-----11--------
651058ChevalierTrypanosoma brucei contains a ...Trypanosoma bruceiEur. J. Biochem.2671464-14722000--1----2---1-5--1--11-11-------1-1---11------2---1---1-11-11-------1------
651088NairnCharacterization of active-sit ...Schizosaccharomyces pombeEur. J. Biochem.2677065-707420002-1-7--7---1-3--------2------------2-1--7----7---1--------2---------------
649101CrowhurstStructure of a phosphoglycerat ...Saccharomyces cerevisiaeActa Crystallogr. Sect. D551822-182619991--1-------1-3--1-----1------------1---1---------1---1----1---------------
649656Walter-The role of the C-terminal reg ...Saccharomyces cerevisiae, Schizosaccharomyces pombeBiochem. J.33789-9519994-2-32-6---2-2--2-----42---4---1---4-21-32---6---2---2----42---4----------
652790RigdenSulphate ions observed in the ...Saccharomyces cerevisiaeJ. Mol. Biol.2861507-151719991-113--4---1-3--------1----4-------1-1-13----4---1--------1----4----------
652799RigdenPolyanionic inhibitors of phos ...Saccharomyces cerevisiae, Schizosaccharomyces pombeJ. Mol. Biol.289691-69919992--1-1122---2-5--2-----3----2----12--2---1-1-12122---2---2----3----2----------
653052ChanderStructural studies on a 2,3-di ...Geobacillus stearothermophilusJ. Struct. Biol.126156-1651999--11---1-1-1-3--1---2-11----1--1-1---111-----1-1-1---1--2-11----1--1------
3216RigdenThe 2.3 A X-ray crystal struct ...Saccharomyces cerevisiaeJ. Mol. Biol.276449-45919981--1-------1-4--1-----11-----------1---1---------1---1----11--------------
650753ChanderThe enzymatic activity of phos ...Bacillus subtilis, Clostridium perfringens, Micrococcus luteus, Planococcus citreus, Sporosarcina ureae, Staphylococcus saprophyticus, Streptomyces coelicolorCan. J. Microbiol.44759-7671998------16-9-7-12--7---7-7-----77-7------7----1-6-9-7---7--7-7-----77--------
3217DuranyPhosphoglycerate mutase, 2,3-b ...Homo sapiensBr. J. Cancer761139-114919971----------1-2-----25-2------------1-------------1-----25-2---------------
3218DuranyPhosphoglycerate mutase, 2,3-b ...Homo sapiensBr. J. Cancer75969-9771997-------------1-----41----------------------------------41-----------------
3219PriceThe reaction of phosphoglycera ...Schizosaccharomyces pombeBiochem. Soc. Trans.24324S19961-----1------2--------1------------1-------1--------------1---------------
3220DuranyDistribution of phosphoglycera ...Homo sapiens, Oryctolagus cuniculus, Rattus norvegicusComp. Biochem. Physiol. B114217-2231996-------------7-----24-----------------------------------24------------------
3221NairnPhosphoglycerate mutase from S ...Schizosaccharomyces pombeBiochim. Biophys. Acta129669-7519961-1----------4------2-11-----------1-1------------------2-11--------------
3222WangLily cofactor-independent phos ...Lilium longiflorumPlanta200343-35219961-------3----4-----4---------------1----------3--------4------------------
3223Grana2,3-Bisphosphoglycerate-indepe ...Homo sapiens, More, Prunus dulcis, Zea maysComp. Biochem. Physiol. B112287-2931995-------------10-----2-----------------------------------2------------------
3224KuhnCooperative Manganese (II) act ...Bacillus megateriumArch. Biochem. Biophys.32035-421995---------1---2-----1---------------------------1-------1------------------
3225MorrisIsolation and sequence analysi ...Pseudomonas syringaeJ. Bacteriol.1771727-17331995--1----------7--------1--------------1--------------------1---------------
3226Perez de la OssaIsolation and characterization ...Zea maysBiochem. Biophys. Res. Commun.2031204-120919941-1----------3-----1---------------1-1-----------------1------------------
3227EstellerThyroid hormone stimulates pho ...Rattus norvegicusLife Sci.54533-5381994-------------3-----6-----------------------------------6------------------
3228HuangHigher-plant cofactor-independ ...Nicotiana tabacum, Ricinus communisPlant Mol. Biol.231039-10531993--1-----22---7--1--41----------------1--------22-----1-41-----------------
677798KuhnManganese(II) activation of 3- ...Bacillus megateriumArch. Biochem. Biophys.306342-3491993------1--2---3----1------------------------1---2------1-------------------
3229WhitePhosphoglycerate mutase from S ...Streptomyces coelicolorJ. Bacteriol.174434-44019921-1---111-1--5--1---1-11-----------1-1-----1-11-1----1--1-11--------------
3230WhiteDevelopment of a mutagenesis, ...Saccharomyces cerevisiaeEur. J. Biochem.207709-71419921-1-1--2-----3--1----------2-------1-1--1----2-------1---------2----------
3231WhiteMutase versus synthase: the ph ...Saccharomyces cerevisiaeBiochem. Soc. Trans.1825719901---2--6---1-1---1----3----3-------1----2----6---1--------3----3----------
3232UrenaLocation of phosphoglycerate m ...Rattus norvegicusEur. J. Cell Biol.51151-1561990--------3-1--3-----2--------------------------3-1------2------------------
3233EdwardsPurification of human muscle p ...Homo sapiensJ. Chromatogr.490424-4311989-------------2-----3-----------------------------------3------------------
3234GranaPurification, characterization ...Zea maysEur. J. Biochem.186149-1531989------22--1--5--1--21111----11-------------2-2--1----1-21111----11--------
3235BatkeComplex of brain D-phosphoglyc ...Bos taurusArch. Biochem. Biophys.264510-5181988-------------2-----1-----------------------------------1------------------
3236CastellaImmunological properties of ra ...Rattus norvegicusBiochim. Biophys. Acta95697-1021988-------------3--1--2--11-----------------------------1-2--11--------------
3237McAleese-Cofactor-independent monophosp ...Neurospora crassaBiochem. Soc. Trans.16558-55919881----1----1--1--1------1-----------1-----1------1----1-----1--------------
3238JohnsonDo metal ions promote the re-a ...Emericella nidulans, Neurospora crassa, Triticum aestivumBiochem. J.252111-1171988------4---1--6--1-3--1-2-------------------4----1----13--1-2--------------
3261SakodaIsolation of a cDNA encoding t ...Homo sapiensJ. Biol. Chem.26316899-169051988--1----------4-----1-----------------1-----------------1------------------
3239Johnson-Co-factor-independent phosphog ...Bacillus megaterium, Bacillus subtilis, Cyberlindnera jadinii, Enterobacter aerogenes, Escherichia coli, Oryctolagus cuniculus, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Solanum tuberosum, Vigna radiataBiochem. Soc. Trans.1587819874-----26------10---------------------4-------26------------------------------
3240Johnson-How similar are the phosphogly ...Oryctolagus cuniculus, Saccharomyces cerevisiaeBiochem. Soc. Trans.15247-24819872-----4------2---221---1-----------2-------4----------21---1--------------
3262ShanskeIsolation of cDNA encoding the ...Homo sapiensJ. Biol. Chem.26214612-146171987--1----------4-----1-----------------1-----------------1------------------
3241PawlukIsolation and properties of th ...Zymomonas mobilisBiochem. J.238275-28119861------1--1--4--1---1-11-----------1---------1--1----1--1-11--------------
3242PrehuPurification of the M-type pho ...Oryctolagus cuniculusJ. Chromatogr.360203-2101986-------------3--1--31-1------------------------------1-31-1---------------
3243BothaIsozymes of phosphoglyceromuta ...Ricinus communisArch. Biochem. Biophys.24596-10319861-----14212--3--1--221----2-3-3----1-------1-4212----1-221----2-3-3-------
3244SmithWheat germ phosphoglycerate mu ...Triticum aestivumBiochem. Biophys. Res. Commun.131743-7491985------5------3--1--11----------------------5---------1-11-----------------
3245RosaPurification of human erythroc ...Homo sapiensJ. Chromatogr.285203-2091984-------------2--1--21--------------------------------1-21-----------------
3246KulbeSimultaneous purification of g ...Sus scrofaMethods Enzymol.90498-5111982-------------2--1--41-1------------------------------1-41-1---------------
3247ScopesPurification of all glycolytic ...Oryctolagus cuniculusMethods Enzymol.90479-4901982-------------1--1--1--1------------------------------1-1--1---------------
3248BartronsPurification and characterizat ...Sus scrofaBiochim. Biophys. Acta708167-1771982------12--1--3--1--2--11--1-11-------------1-2--1----1-2--11--1-11--------
3213RoseThe enzymology of 2,3-bisphosp ...Gallus gallus, Homo sapiens, Oryctolagus cuniculus, Saccharomyces cerevisiae, Sus scrofa, Triticum aestivumAdv. Enzymol. Relat. Areas Mol. Biol.51211-25319804------------6---------------------4--------------------------------------
3249SinghPurification and properties of ...Bacillus megaterium, Bacillus subtilisJ. Bacteriol.1371024-102719792-----41--1--4--1--2---1----1------2-------4-1--1----1-2---1----1---------
3250WatabePurification and properties of ...Bacillus subtilisJ. Bacteriol.137773-77819792-----92-----3------1-2-----11-----2-------9-2----------1-2-----11--------
3251IkuraImmunochemical and enzymatic p ...Homo sapiensEur. J. Biochem.8923-311978------11-----2--1--2-----------------------1-1-------1-2------------------
3252GatehousePhosphoglycerate mutase from w ...Triticum aestivumBiochemistry163045-305219771--1------2--3--1--1-1--------1----1---1--------2----1-1-1--------1-------
3253HillPurification and characterizat ...Hyphomicrobium sp., Pseudomonas sp.J. Gen. Microbiol.96185-19319762------4-----7--2---224---4-2------2---------4-------2--224---4-2---------
3254SheibleyIsolation and partial characte ...Homo sapiensJ. Biol. Chem.2516699-670419761---------1--3--1--211-1----1------1------------1----1-211-1----1---------
3255HassA comparison of some of the ph ...Homo sapiensBiochem. Biophys. Res. Commun.72976-9831976----------1--1-----1---1------------------------1------1---1--------------
3256HartmanDetection of an essential sulf ...Oryctolagus cuniculusJ. Biol. Chem.2514565-45691976------1------3-----2-----------------------1-----------2------------------
3257SasakiSubunit structure and multifun ...Saccharomyces cerevisiaeEur. J. Biochem.66523-5331976------1------3--1---1----------------------1---------1--1-----------------
3258GrisoliaPhosphoglycerate mutase from y ...Gallus gallus, Saccharomyces cerevisiae, Sus scrofaMethods Enzymol.42435-4501975-------------5--3--73-----3--------------------------3-73-----3-----------
3259Grisolia-Phosphoglycerate mutase from w ...Oryza sativa, Triticum aestivumMethods Enzymol.42429-43519752------2-----2--2--21-2----2--1----2---------2-------2-21-2----2--1-------
3260D'AlessioPhosphoglycerate kinase, phosp ...Escherichia coliMethods Enzymol.42139-14419751---------1--2--1---1--------------1------------1----1--1-----------------
3214Ray-Phosphomutases ...Gallus gallus, Oryctolagus cuniculus, Saccharomyces cerevisiae, Sus scrofa, Triticum aestivumThe Enzymes, 3rd Ed. (Boyer, P.D., ed.)6407-4771972-----2-------5------------4--------------2--------------------4-----------
3215Grisolia-Phosphoglyceric acid mutases ...Saccharomyces cerevisiae, Triticum aestivumMethods Enzymol.5236-2421962------2------2------221-----2--------------2------------221-----2---------