The Structure of Escherichia coli ATP-phosphoribosyltransferase: Identification of Substrate Binding Sites and Mode of AMP Inhibition

Lohkamp, Bernhard; McDermott, Gerry; Campbell, Samantha A; Coggins, John R.; Lapthorn, A.J.

doi:10.1016/j.jmb.2003.12.020

Cited by 54 publications

(92 citation statements)

References 35 publications

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“…The long and short form ATP-PRTs differ in quaternary structure and mechanism of allostery, although they share a common catalytic core [4,5,12,13]. …”

Section: Discussionmentioning

confidence: 99%

Independent catalysis of the short form HisG from Lactococcus lactis

et al. 2016

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Edited by Michael IbbaATP-phosphoribosyltransferase (ATP-PRT) catalyses the first step of histidine biosynthesis. Two different forms of ATP-PRT have been described; the homo-hexameric long form, and the hetero-octameric short form. Lactococcus lactis possesses the short form ATP-PRT comprising four subunits of HisG S , the catalytic subunit, and four subunits of HisZ, a histidyl-tRNA synthetase paralogue. Previous studies have suggested that HisG S requires HisZ for catalysis. Here, we reveal that the dimeric HisG S does display ATP-PRT activity in the absence of HisZ. This result reflects the evolutionary relationship between the long and short form ATP-PRT, which acquired allosteric inhibition and enhanced catalysis via two divergent strategies.

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“…The long and short form ATP-PRTs differ in quaternary structure and mechanism of allostery, although they share a common catalytic core [4,5,12,13]. …”

Section: Discussionmentioning

confidence: 99%

Independent catalysis of the short form HisG from Lactococcus lactis

et al. 2016

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“…This domain arrangement is similar to those of TmHisGS 12 and LlHisGS, 11 and to the catalytic domains of HisGL. 8,19 Each pair of PaHisGS makes up a homodimer in which subunits interact in a head-totail arrangement ( Figure 1B). An interface score of 1 was calculated for this interaction, suggesting that it is responsible for homodimer formation.…”

Section: Purification Ofmentioning

confidence: 99%

Kinetics and Structure of a Cold-Adapted Hetero-Octameric ATP Phosphoribosyltransferase

Stroek

Talbot²,

Glok³

et al. 2017

Biochemistry

112

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ATP-phosphoribosyltransferase (ATPPRT) catalyses the first step in histidine biosynthesis, the condensation of ATP and 5-phospho--D-ribosyl-1-pyrophosphate to generate N 1 -(5-phospho--D-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisGL, is a single polypeptide chain with catalytic and regulatory domains. The short form, HisGS, lacks a regulatory domain, and cannot bind histidine. HisGS instead is found in complex with a regulatory protein, HisZ, constituting the ATPPRT holoenzyme. HisZ triggers HisGS catalytic activity while rendering it sensitive to allosteric inhibition by histidine. Until recently, HisGS was thought to be catalytically inactive without HisZ. Here, recombinant HisGS and HisZ from the psychrophilic bacterium Psychrobacter arcticus were independently overexpressed and purified. The crystal structure of P. arcticus ATPPRT was solved at 2.34-Å resolution, revealing an equimolar HisGS-HisZ hetero-octamer. Steady-state kinetics indicate that both ATPPRT holoenzyme and HisGS are catalytically active. Surprisingly, HisZ confers only a modest 2-to 4-fold increase in kcat.Reaction profiles for both enzymes are indistinguishable by 31 P-NMR, indicating that the same reaction is catalysed. Temperature dependence of kcat shows deviation from Arrhenius behaviour at 308 K with the holoenzyme. Interestingly, such deviation is detected only at 313 K with HisGS. Thermal denaturation by CD spectroscopy resulted in Tm's of 312 K and 316 K for HisZ and HisGS, respectively, suggesting that HisZ renders the ATPPRT complex more thermolabile. This is the first characterisation of a psychrophilic ATPPRT. 4Adenosine 5ʹ-triphosphate phosphoribosyltransferase (ATPPRT) (EC 2.4.2.17) catalyses the reversible Mg 2+ -dependent reaction between adenosine 5ʹ-triphosphate (ATP) and(PR-ATP) and inorganic pyrophosphate (PPi) (Scheme 1), the first step in histidine biosynthesis. 1 The chemical equilibrium of the reaction strongly favours reactants, 2 and the enzyme is allosterically inhibited by histidine. 1 In addition to being a model for understanding allostery, 2-4 ATPPRT is of biotechnological interest as a tool for histidine production, provided that histidine feedback inhibition can be overcome. [5][6][7] Two forms of ATPPRT, encoded by the hisG gene, are found in nature. Fungi, plants, and most bacteria possess a long, homo-hexameric protein, HisGL, each subunit consisting of two domains that make up the catalytic core and a C-terminal regulatory domain that mediates feedback inhibition by histidine. 8 Some bacteria and archaea have a short version of the protein, HisGS, which lacks the C-terminal regulatory domain and is insensitive to histidine. In these organisms, a catalytically inactive regulatory protein, HisZ, the product of the hisZ gene, is present. 9 HisZ, which shares a common ancestry with histidyl-tRNA synthetase (HisRS), binds HisGS to form ...

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“…For example, the K m ATP for the S. typhimurium enzyme was reported as 110-200 μM (1,20), while values of 600 μM and 510 μM were determined the two isozymes of A. thalia (24). Non-physiological concentrations of ATP in excess of 15 mM were inhibitory to ATP-PRT, which may reflect a competition by ATP for the PRPP binding site, as proposed for AMP (14). This phenomenon remains to be investigated in more depth.…”

Section: Steady State Kinetic Parameters For the Prt Reaction Catalyzmentioning

confidence: 98%

“…Not surprisingly, the value of K i His detemined here is nearly equal to the histidine Michaelis constant for histidyl-tRNA synthetase (K m His =35 μM), which possesses a structurally similar binding pocket (35). In view of the structural differences between the histidine binding domains of the two enzyme families (13,14,18,19), this nearly identical value of the K i for histidine for the long and short forms is striking. The higher K i His (350 μM) reported for the T. maritima enzyme (18) represents a significant outlier from these values, but could be a consequence of performing the measurement at 20 °C, below the physiologically optimal temperature for Thermatoga, which is 80 °C It is notable that the two While the parameters for PRPP and histidine were essentially identical between the two ATP-PRT families, K m ATP differed by a factor of more than ten (Table 1).…”

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confidence: 96%

“…These empirical and theoretical observations illustrate why selective pressures may have led to complex regulatory features in ATP-PRT that allow it to control histidine biosynthesis at the metabolic level. The principal goal of this study was to explore the functional differences of the two distinct forms of ATP-PRT, both of which appear to share a common evolutionary ancestry (12), yet possess different quaternary structures (13,14,18,19). Identification of functional features that separate the two classes should help to account for their persistence in contemporary organisms.…”

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Substrate Recognition by the Hetero-Octameric ATP Phosphoribosyltransferase from Lactococcus lactis

2006

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Two families of ATP phosphoribosyl transferases (ATP-PRT) join ATP and 5-phosphoribosyl-1 pyrophosphate (PRPP) in the first reaction of histidine biosynthesis. These consist of a homohexameric form found in all three kingdoms, and a hetero-octameric form largely restricted to bacteria. Hetero-octameric ATP-PRTs consist of four HisG S catalytic subunits related to periplasmic binding proteins, and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. To clarify the relationship between the two families of ATP-PRTs, and among phosphoribosyltransferases in general, we determined the steady state kinetics for the heterooctameric form, and characterized the active site by mutagenesis. The K m PRPP (18.4 ± 3.5 μM) and k cat (2.7 ± 0.3 sec −1 ) values for the PRPP substrate are similar to those of hexameric ATP-PRTs, but the K m for ATP (2.7 ± 0.3 mM) is 4-fold higher, suggestive of tighter regulation by energy charge. Histidine and AMP were determined to be non-competitive (K i = 81.1 μM) and competitive (K i = 1.44 mM) inhibitors, respectively, with values that approximate their intracellular concentrations. Mutagenesis experiments investigating the side chains recognizing PRPP showed that 5′ phosphate contacts (T159A and T162A) had the largest (25-and 155-fold) decreases in k cat /K m , while smaller decreases were seen with mutants making cross subunit contacts (K50A and K8A) to the pyrophosphate moiety, or contacts to the 2′ OH. Despite their markedly different quaternary structures, hexameric and hetero-octameric ATRP-PRTs exhibit similar functional parameters, and employ mechanistic strategies reminiscent of the broader PRT superfamily.ATP phosphoribosyltransferase (ATP-PRT; E. C. 2.4.2.17) catalyzes the first and highly regulated step of histidine biosynthesis, which involves nucleophillic attack of the N1 of ATP on C1′ of 5-phosphoribosyl-1 pyrophosphate (PRPP) to form N-1-(5′-phosphoribosyl)-ATP (PR-ATP, Figure 1A) (1). The resulting product is converted through an additional nine reactions into histidine by a pathway that is regulated both by its end product and by AMP and ADP (2). The tight regulation of this pathway (reviewed in (3)), reflects the high energetic costs associated with histidine synthesis, and the need to dramatically slow pathway flux when histidine is present in the growth media (4). Superimposed on top of metabolic control of † This work was supported by N.I.H. grant GM54899 (CSF) histidine biosynthesis is genetic regulation of the expression of histidine biosynthetic enzymes, by use of the classic attenuation mechanism (reviewed in (5)).ATP-PRT is a member of the phophoribosyltransferase (PRT) superfamily of enzymes, all of whom share a common chemistry that involves transfer of the phosphoribosyl group to a nucleotide base or, in the case of glutamine phosphoribosyl pyrophosphate amidotransferase, to free ammonia generated on the enzyme (6). PRTs are found in many essential pathways, including biosynthesis and salvage of nucleotides, and the synthesis of cofac...

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The Structure of Escherichia coli ATP-phosphoribosyltransferase: Identification of Substrate Binding Sites and Mode of AMP Inhibition

Cited by 54 publications

References 35 publications

Independent catalysis of the short form HisG from Lactococcus lactis

Independent catalysis of the short form HisG from Lactococcus lactis

Kinetics and Structure of a Cold-Adapted Hetero-Octameric ATP Phosphoribosyltransferase

Substrate Recognition by the Hetero-Octameric ATP Phosphoribosyltransferase from Lactococcus lactis

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