PGD Human
Description
Introduction to PGD Human
Phosphogluconate dehydrogenase (PGD) is a critical enzyme in human cellular metabolism. It is classified as Gene 5226 in taxonomic databases and is specifically found in Homo sapiens. The enzyme is also known by several synonyms including 6PGD, PGDH, and 6-phosphogluconate dehydrogenase decarboxylating .
PGD functions as a key component of the pentose phosphate pathway (also called the pentose phosphate shunt), serving as the second dehydrogenase in this important metabolic process. This pathway runs parallel to glycolysis and is essential for generating NADPH and pentoses, which are vital for numerous cellular functions .
The PGD gene has been well-characterized, with its creation date in reference databases dating back to September 2016, and modifications continuing through March 2025, indicating ongoing research interest in this enzyme .
2.1. Molecular Structure and Physical Characteristics
PGD Human is a single, non-glycosylated polypeptide chain containing 483 amino acids in its native form. The recombinant version typically includes additional amino acids such as a His-Tag at the N-terminus, bringing the total to 503 amino acids with a molecular mass of approximately 55.3 kDa .
The enzyme is predicted to enable NADP binding activity, which is essential for its function as a dehydrogenase. Structurally, PGD is localized in several cellular compartments, including the extracellular exosome and nucleus, allowing it to participate in various metabolic processes throughout the cell .
When produced as a recombinant protein, PGD Human appears as a sterile filtered clear colorless solution. For research applications, it is typically formulated in a buffer containing 10% Glycerol, 1mM DTT, 0.1M NaCl, and 20mM Tris-HCl at pH 8.0 .
2.3. Protein Isoforms and Structure
Research has identified multiple isoforms of PGD in humans. The primary isoforms documented in reference databases include:
| Isoform | UniProt ID | RefSeq Accession |
|---|---|---|
| Isoform 1 | P52209-1 | NP_002622.2 |
| Isoform 2 | P52209-2 | NP_001291381.1 |
Several transcript variants encoding different isoforms have been found for the PGD gene, indicating complex regulation and potentially diverse functions of this enzyme in human metabolism .
3.1. Enzymatic Activity
PGD catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and carbon dioxide (CO₂), with the concomitant reduction of NADP to NADPH. This reaction represents a critical step in the pentose phosphate pathway .
The specific activity of recombinant PGD Human is typically greater than 10 units per milligram. One unit is defined as the amount of enzyme that will oxidize 1.0 micromole of 6-phospho-D-gluconate to D-ribulose 5-phosphate per minute at pH 8.0 at 25°C, in the presence of β-NADP .
3.2. Metabolic Significance
The pentose phosphate pathway serves two essential functions in cellular metabolism:
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Production of NADPH: This reduced form of nicotinamide adenine dinucleotide phosphate is required for many biosynthetic reactions, particularly lipid synthesis. NADPH also maintains glutathione in its reduced form, which is essential for cellular protection against oxidative damage .
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Generation of pentoses: The pathway produces ribose-5-phosphate, which is necessary for nucleic acid biosynthesis. This makes the pathway critical for cellular growth and division .
As the second dehydrogenase in this pathway, PGD plays a vital role in both of these functions. The enzyme's activity directly contributes to the cellular pool of NADPH, making it a key player in redox homeostasis and biosynthetic processes .
4.1. PGD Deficiency
PGD deficiency is generally asymptomatic, and the inheritance pattern of this disorder is autosomal dominant. This relatively mild clinical presentation contrasts with many other enzyme deficiencies that cause more severe symptoms .
4.2. Metabolic Effects
PGD deficiency has been observed to alter the levels of other enzymes in erythrocytes (red blood cells). Specifically, it:
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Raises the activity levels of erythrocyte pyruvate kinase
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Decreases glutathione synthetase activity
These changes can potentially result in hemolysis, highlighting the importance of PGD in maintaining red blood cell integrity .
4.3. Evolutionary Conservation
The PGD gene has been remarkably conserved throughout evolution, with homologs found in numerous species including:
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Mammals: Norway rat, house mouse, rabbit, horse, domestic cattle, dog, sheep, pig
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Other vertebrates: chicken, zebrafish
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Specialized species: platypus, white-tufted-ear marmoset
This high degree of conservation across diverse species suggests the fundamental importance of PGD in cellular metabolism throughout the animal kingdom .
5.1. Production Methods
Recombinant PGD Human is typically produced in Escherichia coli expression systems. The resulting protein is a single, non-glycosylated polypeptide chain containing the 483 amino acids of the native human PGD, fused to a 20 amino acid His-Tag at the N-terminus to facilitate purification .
The recombinant protein is purified using proprietary chromatographic techniques, resulting in a product with greater than 90% purity as determined by SDS-PAGE. This high-purity preparation is essential for accurate research applications and enzymatic assays .
Product Specs
Q&A
What distinguishes preimplantation genetic diagnosis (PGD) from other genetic testing methods?
PGD is a laboratory procedure performed in conjunction with in vitro fertilization (IVF) that enables the genetic assessment of embryos prior to implantation. Unlike prenatal testing methods that analyze fetal cells during pregnancy, PGD involves the biopsy of embryonic cells at the preimplantation stage, typically when the embryo has reached the six-to-eight-cell stage (day three of development). This approach allows for the identification of genetic conditions before pregnancy is established, offering a unique temporal advantage in reproductive genetics.
The procedure involves several methodologically distinct steps:
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Oocyte maturation and retrieval through controlled ovarian stimulation
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Fertilization using intracytoplasmic sperm injection (ICSI)
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Embryo culture to the appropriate developmental stage
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Embryo biopsy with removal of one to two cells
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Genetic analysis of the biopsied cells
How has the scientific understanding and terminology of PGD evolved historically?
The concept underlying PGD has undergone significant terminological evolution since its initial demonstration in animals in 1968. Before its clinical application in humans in 1990, researchers referred to this technique using various terms:
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"Embryo sexing" (primarily in animal studies)
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"Preimplantation diagnosis"
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"Embryo biopsy"
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"Prenatal diagnosis before implantation"
Contemporary literature has standardized terminology, with "preimplantation genetic diagnosis (PGD)" now specifically referring to the clinical technique of diagnosing genetic characteristics in preimplantation embryos without compromising viability or further embryonic development. More recently, the term "preimplantation genetic testing for monogenic disorders" (PGT-M) has been adopted to refer to testing for specific single-gene disorders.
What are the key diagnostic strategies employed in current PGD research, and how do they differ methodologically?
Modern PGD research employs two primary diagnostic strategies following trophectoderm (TE) biopsy:
Target Amplification Approach:
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Utilizes multiplex PCR for direct mutation identification
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Simultaneously analyzes genetic markers linked to the condition
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Particularly effective for known single-gene disorders
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Requires less computational analysis than whole-genome approaches
Whole-Genome Amplification (WGA) Approach:
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Provides comprehensive genetic information
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Can be followed by several analytical methods:
Both approaches rely on haplotyping principles to determine whether embryos have inherited risk-associated or wild-type alleles. This process requires preclinical work-up, including genotyping of SNP markers near the gene of interest in DNA samples from the couple and family members with known genetic status.
How do researchers address data contradictions between different PGD analytical approaches?
A significant methodological challenge in PGD research concerns contradictions between data derived from different analytical approaches. For example, direct oocyte chromosome studies and PGD analyses provide divergent information regarding the distribution of aneuploidy-causing mechanisms during maternal meiosis:
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Conventional direct analysis of unfertilized oocytes suggests certain patterns of non-disjunction (ND) and precocious division (PD) of chromosomes
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Polar body analyses yield contradictory data compared to DNA polymorphism studies regarding the distribution of first and second meiotic division errors
Addressing these contradictions requires:
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Systematic comparative analyses between methodologies
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Standardization of analytical protocols
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Integration of multiple data types when making clinical interpretations
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Increased awareness of these discrepancies when making decisions based on PGD results
These contradictions highlight the importance of methodological transparency and cautious interpretation of PGD data in both research and clinical contexts.
What methodological approaches are used for haplotyping in PGD/PGT-M research?
Haplotyping is a fundamental methodological component of PGD/PGT-M that enables researchers to determine which chromosome carries a disease-causing mutation. Current methodological approaches include:
STR-based Analysis:
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Short tandem repeats (STRs) are used as polymorphic markers
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A single informative STR is equivalent to three informative SNPs
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Analysis conducted via capillary electrophoresis
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Allows discrimination of parental haplotypes
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Particularly useful for chromosomes affected by specific mutations
SNP-based Analysis:
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Single nucleotide polymorphisms are more abundant (one SNP every 300-1000 bp)
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Generally easier to interpret than STRs
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Better suited for high-throughput analysis
Both approaches require extensive preclinical setup to establish high-risk (mutant) and low-risk haplotypes, making PGT-M a resource-intensive procedure requiring substantial preliminary family studies.
How do researchers optimize experimental protocols for detecting both monogenic diseases and chromosomal abnormalities simultaneously?
Integrated approaches for simultaneous detection of monogenic diseases and chromosomal abnormalities represent an advanced methodological frontier in PGD research. Two innovative strategies have emerged:
"One PGT solution":
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Employs next-generation sequencing with Multiple Displacement Amplification (MDA)
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Enables identification of both monogenic diseases and numerical/structural chromosomal abnormalities
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Offers comprehensive genetic assessment in a single analytical workflow
TaqMan Assay Integration:
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Combines TaqMan assays for mutations with informative SNPs
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Allows addition of Copy Number Variation (CNV) assays
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Enables simultaneous detection of aneuploidies (combined PGT-M and PGT-A)
These integrated approaches improve efficiency but require careful validation to ensure diagnostic accuracy across multiple genetic parameters.
What are the essential components of experimental design when conducting PGD research?
Effective experimental design in PGD research follows systematic principles that enhance validity and reproducibility:
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Variable Definition:
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Hypothesis Formulation:
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Treatment Design:
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Subject Assignment:
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Measurement Planning:
Additionally, PGD research requires particular attention to selecting representative samples and controlling extraneous variables that might influence results.
How should researchers approach experimental validation of new PGD/PGT techniques?
Validation of novel PGD/PGT techniques requires rigorous experimental approaches to ensure diagnostic accuracy and clinical applicability:
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Analytical Validation:
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Determination of technical sensitivity and specificity
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Assessment of reproducibility across different operators and laboratories
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Comparison with established "gold standard" methods
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Analysis of amplification efficiency and allele dropout rates
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Clinical Validation:
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Correlation of PGD results with established diagnostic methods
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Follow-up studies comparing PGD predictions with actual outcomes
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Systematic collection of data on diagnostic discrepancies
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Protocol Optimization:
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Systematic testing of procedural variations
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Documentation of protocol refinements based on experimental outcomes
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Establishment of quality control metrics for ongoing monitoring
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Proper validation is particularly critical given the complexity of chromosomal rearrangements and the technological limitations that can influence result accuracy and reliability in PGT for structural rearrangements (PGT-SR).
How do researchers address the limitations of working with minimal genetic material in PGD?
Working with the minimal genetic material available from embryo biopsies presents significant methodological challenges that researchers address through several specialized approaches:
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Whole Genome Amplification Strategies:
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Multiple Displacement Amplification (MDA)
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Degenerate Oligonucleotide Primed PCR (DOP-PCR)
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PicoPLEX/SurePlex amplification
Each method offers different advantages in terms of genome coverage, amplification bias, and error rates when working with single or few cells.
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Quality Control Measures:
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Implementation of stringent contamination controls
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Assessment of amplification efficiency
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Monitoring of allele dropout rates
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Inclusion of internal control markers for verification
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Bioinformatic Approaches:
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Development of specialized algorithms for analyzing limited-source DNA
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Computational methods for distinguishing true variants from amplification artifacts
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Statistical models accounting for technical variability in single-cell genetics
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These methodological adaptations have transformed what was once considered an insurmountable technical limitation—"no single-cell diagnostic techniques available" requiring cell culture for sufficient DNA—into routine clinical practice through innovations in molecular biology and bioinformatics.
What methodological approaches help researchers distinguish between technical artifacts and true genetic findings in PGD?
Distinguishing technical artifacts from true genetic findings represents a critical methodological challenge in PGD research due to the limited genetic material available and amplification requirements. Researchers employ several strategies to address this challenge:
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Linkage Analysis Approaches:
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Contamination Detection Protocols:
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Technical Artifact Identification:
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Assessment of allele dropout patterns
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Identification of preferential amplification signatures
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Differentiation between genuine mosaicism and technical variability
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Confirmatory Testing:
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Use of orthogonal technological approaches for verification
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Implementation of repeat testing protocols for ambiguous results
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Integration of multiple data types when making diagnostic determinations
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These methodological approaches are particularly important because clinical decisions regarding embryo selection are made based on PGD results, making accurate distinction between artifacts and true findings essential for research translation.
Product Science Overview
PGD is a protein-coding gene, and the human recombinant form is typically produced in E. coli for research and therapeutic purposes . The enzyme’s activity is essential for cellular processes that require NADPH, such as fatty acid synthesis and the maintenance of reduced glutathione levels, which protect cells from oxidative damage .
Recombinant human PGD is produced using E. coli expression systems. The recombinant protein is often tagged with a His-tag for purification purposes and is supplied in a carrier-free form to avoid interference in experimental applications . The enzyme’s activity is measured by its ability to dehydrogenate 6-phosphogluconic acid, with a specific activity greater than 6000 pmol/min/μg .
