Difference between revisions of "Os08g0126300"
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<ref name="ref1"> Yueh-Chu Tien;Phimonphan Chuankhayan;Yen-Chieh Huang;Chung-De Chen;Jahan Alikhajeh;Shou-Lin Chang;Chun-Jung Chen. Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis. Plant Molecular Biology[J], 2012, 80(4-5): 389-403.</ref> | <ref name="ref1"> Yueh-Chu Tien;Phimonphan Chuankhayan;Yen-Chieh Huang;Chung-De Chen;Jahan Alikhajeh;Shou-Lin Chang;Chun-Jung Chen. Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis. Plant Molecular Biology[J], 2012, 80(4-5): 389-403.</ref> | ||
| + | |||
<ref name="ref2"> Pillai, M. A., et al.Molecular cloning, characterization, expression and chromosomal location of OsGAPDH, a submergence responsive gene in rice (Oryza sativa L.). Theoretical and Applied Genetics[J], 2002, 105(1): 34-42.</ref> | <ref name="ref2"> Pillai, M. A., et al.Molecular cloning, characterization, expression and chromosomal location of OsGAPDH, a submergence responsive gene in rice (Oryza sativa L.). Theoretical and Applied Genetics[J], 2002, 105(1): 34-42.</ref> | ||
Revision as of 03:38, 11 June 2014
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Contents
Annotated Information
Function
Glyceraldehyde-3-phosphate dehydrogenase involved in the ubiquitous glycolysis, catalyzes the oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate (BPG) using nicotinamide adenine dinucleotide (NAD) as an electron acceptor.
the following reaction: G3P + NAD + Pi → BPG + NADH
The homotetramer form of GADPH in vivo is proved to attribute many and diverse non-glycolytic functions, such as membrane fusion, phosphotransferase activity.[1].
Mutation
Phe37 plays a crucial role in stabilizing NAD binding or intermediating of apoholo transition, resulting in a greater NAD-dependent catalytic efficiency using site-directed mutagenesis
The kinetic parameters of OsGAPDH showed that the mutation on Phe37 has a significant effect on the catalytic rate and NAD specificity, but does not lead to NADP-dependent activity of OsGAPDH.
Wild type OsGAPDH exhibited the fluorescence intensity with a linear decrease, revealing that the binding of NAD to each subunit induced the same decrease of the fluorescence intensity.
Asp35 and Pro193 of OsGAPDH are conserved residues for the NAD specificity. The mutation F37T, F37L and F37G provid the evidence to elucidate that Phe37 is one key residue for catalysis as its single substitutions gave extremely low activities compared with wild-type OsGAPDH.
In contrast, the dissociation constants K for NAD and NADH binding were increased in the following order: wild type\F37G\F37T\F37L (Table 7). The result supports that a substitution of Phe37 for small aliphatic (Gly or Leu) or polar (Thr) residues could almost abolish the NAD-binding affinity to attenuate the catalytic efficiency of OsGAPDH
The smaller side chains of Gly, Leu and Thr might not form a bottleneck or hold NAD stably into the coenzyme-binding site, resulting in attenuated NAD binding affinities and catalytic efficiency.
According to this apo-holo transition mechanism, a lack of the bottleneck in F37G, F37L or F37T mutants not only decreases the NAD binding affinity but also retards apo-holo transitions, resulting in a greatly diminished catalytic rate or efficiency of cytosolic OsGAPDH.[1].
Expression
The expressions of the genes OsGAPDH are dramatically induced by anaerobiosis
Northern hybridization using total RNA extracted from several organs showed that OsGAPDH was expressed at a high level in the panicle.
Expression analysis of various environmental stresses and growth hormones indicated a coordinate suppression after cold, salt and exogenous application of mannitol and ethephon treatment. Concomitantly, an increase in mRNA accumulation has been noted on drought, submergence and ABA treatments.
The time-course expression of the OsGAPDH transcript was found out under drought, submergence stress and ABA treatment. For drought treatment the highest rate of OsGAPDH transcript accumulation took place at 12-h treatment. However, a decreased transcript level was noticed on the next day and then the accumulation reached a maximum level after 3-days of drought treatment. A stronger submergence response was observed in the 12-h treatment; subsequently the expression declined progressively. The plant hormone ABA showed strong induction within 1 day of treatment and thereafter the transcript level decreased slightly under 2 and 3 days of treatment
Since purified GAPDH activity was inhibited by ATP, ADP, and the metabolites PEP and PGA, the enzyme activity may be regulated by these metabolites under certain physiological conditions.[2].
Evolution
A multiple amino-acid sequence alignment of OsGAPDH with other GAPDH enzymes from various species, including Homo sapien, Oryctolagus cuniculus, Escherichia coli, Bacillus stearomorphilius and Spinacia oleracea, reveals sequence identities 45–68 % with several conserved regions, especially residues 150–170 for the substrate binding.[1].
the deduced amino acid sequence showed a significant similarity to the sequence of maize and, in other plants, non-reversible glyceraldehyde-3- phosphate dehydrogenase indicated that the enzyme was highly conserved. The rice nr-GAPDH sequence closely resembles nr-GAPDH from Zea mays (accession no X75326; 94% identity), Pisum sativum (accession no X75327; 89% identity), Nicotiana plumbaginifolia (accession no U87848; 88% identity) and Apium graveolens (accession no AF196292; 86% identity)[2].
Extension
The crystal structure of OsGAPDH comprises a homotetramer of four monomers with non-crystallographic symmetries holding each other through hydrogen bonds in an asymmetric unit
The overall structure of the OsGAPDH monomer comprises three domains: a NAD-binding domain (residues 1–153 and 318–337), a catalytic domain (154–180 and 210–317) and an S-loop (181–209) .
Among four monomers of a homotetramer, the monomers A, B and C show the extra definable electron densities for NAD molecules, whereas monomer O exhibits the indistinct electron density[1].
Labs working on this gene
1. Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
2. Institute of Structural Biology and Bioinformatics, National Tsing Hua University, Hsinchu, 30043, Taiwan
3. Department of Physics, National Tsing Hua University, Hsinchu, 30043, Taiwan
6. Department of Food Borne and Diarrheal Diseases, Research Center for Gastroenterology and Liver Diseases, Shaheed Beheshti MC, Velenjak, Shahid Chamran Highway, Tehran, Iran
4. Institute of Biotechnology, National Cheng Kung University, Tainan City, 70101, Taiwan
5. University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City, 70101, Taiwan
6. Department of Low Temperature Science, Hokkaido National Agricultural Experiment Station, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
7. Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China,
References
<references> [1]
Structured Information
| Gene Name |
Os08g0126300 |
|---|---|
| Description |
Similar to Glyceraldehyde-3-phosphate dehydrogenase (Fragment) |
| Version |
NM_001067432.1 GI:115474600 GeneID:4344564 |
| Length |
3782 bp |
| Definition |
Oryza sativa Japonica Group Os08g0126300, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 8:1524413..1528194 |
| Sequence Coding Region |
1524488..1524491,1524625..1524648,1524764..1524864,1525152..1525267,1525360..1525459 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008401:1524413..1528194 source=RiceChromosome08 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008401:1524413..1528194 source=RiceChromosome08 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgggcaagattaagatcggaatcaacggtttcggaaggatcgggaggctcgtggccagggtggccctccagagcgaggatgtcgagctcgtcgccgtcaacgaccccttcatcaccaccgactacatgacctacatgttcaagtacgataccgtgcacggccaatggaagcacagcgacatcaagatcaaggactccaagactctgctcttgggcgagaagccggtcaccgttttcggcatcaggaaccctgacgagattccgtgggctgaggctggtgctgagtatgtcgtggagtccaccggtgtcttcactgacaaggagaaggctgctgctcacttgaagggtggtgccaagaaggttgtcatctctgccccgagcaaagatgctccgatgtttgtctgcggtgtcaacgaggacaagtacacttcagatattgatattgtctcaaatgctagctgcaccacaaactgccttgctcctcttgccaaggtcattcatgacaactttggtattatcgagggtctgatgacaactgttcatgccatcactgccacccaaaagaccgttgatggaccgtccagcaaggactggaggggtggcagggcggccagttttaacatcattcccagcagcactggtgctgccaaagctgttggcaaggttcttcctgatttgaatggcaagcttacgggaatgtccttccgtgttcccactgtcgatgtctcagttgttgatctcacagttagaatcgagaaggctgcctcatatgatgctatcaagagtgctatcaagtctgcatcagagggaaagctcaagggaatcataggatatgttgaggaagacctggtttctactgactttgttggtgacagcaggtcgagcatcttcgacgccaaggctggaattgctcttaacgataactttgtcaagcttgtcgcctggtacgacaacgagtggggttacagcaaccgtgtcatcgacctgatccgccacatggccaagacccagtag</cdnaseq> |
| Protein Sequence |
<aaseq>MGKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMT YMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTG VFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLA PLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKA VGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGII GYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMA KTQ</aaseq> |
| Gene Sequence |
<dnaseqindica>76..79#213..236#352..452#740..855#948..1047#1648..1794#1878..1938#2021..2118#2543..2685#2915..2998#3126..3215#3310..3355#tatccggcttccagacgcttctctcctcctctaatctcaagtctctgtctcgtcgtcctcgcatctccactcgccatgggtaattatgctcacctccgaatcgaattaattcccccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcaggcaagattaagatcggaatcaacggtgagtttgctatctgaattactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtgatttgagtgggggttttttgtgtgtttgggattgtgattttgttcaggtttcggaaggatcgggaggctcgtggccagggtggccctccagagcgaggatgtcgagctcgtcgccgtcaacgaccccttcatcaccaccgactacatggtacgctcttcgatctgtgggtttcaccgtcttcatgtgcagatctagtcgtttgtagggttctacagtggttttagctcagatatacatttgcgtgctcgctcaaagagatgtttagtggttgggagttgttttgattgagatatggcagttaattttcccagatctgagtactttttttcgcatgtttagttgctgaattatgctgtttgctactgcatatggctttgattttcgtgtggtgtgctcacgattgatgaattctatgttggtcgtgtgatttgcagacctacatgttcaagtacgataccgtgcacggccaatggaagcacagcgacatcaagatcaaggactccaagactctgctcttgggcgagaagccggtcaccgttttcggcatcaggtaacttgatattgatattacagcttagatgaaagtaacttgtttatggtagcgagcgtggaactgatgtttgatcctgtgcaatttgaaaggaaccctgacgagattccgtgggctgaggctggtgctgagtatgtcgtggagtccaccggtgtcttcactgacaaggagaaggctgctgctcacttgaaggtattatcactgttgcttttcattccaacaaattggcatattgttacatattgttcccatgggattgcatacaagcaagtaaataatgctatggttatttttaagaattaatggatgtagttagattacaaaatcttacacgattttgctaatgatggacacctttgtgtaaaagcatcattatctaactaaaagaaactaagcaatccatggtttttgattatgcataactaaatgtaggcagagatgtgccacaaggggaaagctcattaaaatttgaagtttatgaaccccagtgatatatgtcaaggtctttgcatttacccaaaaagatttggcctgcaaagttaagagtgactacctaagtcttctaaagttaggatgatgcatcacaaagcagacagctcctaattcttttgccttaatttcttaagtattagcatatataacttatggctttgtgttgtcaatttagttttttttattacttgatgccttgtttatttttactctgaaaagtacttgttgtgcatctcccttgttgcataagttagctatttcggtgcattttttatgcttacatggctgttctgaaaacagggtggtgccaagaaggttgtcatctctgccccgagcaaagatgctccgatgtttgtctgcggtgtcaacgaggacaagtacacttcagatattgatattgtctcaaatgctagctgcaccacaaactgccttgctcctcttgccaaggtatttttctttccgagtgacaattttctactttcagttggacttttggtttggttcttaattgactcgttatcatccaataggtcattcatgacaactttggtattatcgagggtctgatgacaactgttcatgccatcactggtaagactttcttggctttttggcagctaatatgaacatctagatgttctgtaatagctaacgctgatgtacttgttttcagccacccaaaagaccgttgatggaccgtccagcaaggactggaggggtggcagggcggccagttttaacatcattcccagcagcactggtgctgccaaagtacgtcatgaacttcaatgttgtgcatgcacaaccacagttcaaaatcctctttatagttccaataattttgtattctcctgtgttatggggctgcgtatagttttctttttgactttatttgggaatgttaagtagaagacccagtgataatagcaagtaactgcacaaatggcgcgcttgctgatttcagccctagagtttttgttgataaatgagcatgtgcgctgtctttattcaagtatgaattctctctcatgtcctatgacgaattgcttgctgttcatgcttctgttcagagttgtttctggcctgcttagggaaaagggggtgcatgtgggcggtagtttttggttgtgaaagcatgttttgttagtaaaatgggactgcagccttaatgacttctaacatcaatgcattgcaggctgttggcaaggttcttcctgatttgaatggcaagcttacgggaatgtccttccgtgttcccactgtcgatgtctcagttgttgatctcacagttagaatcgagaaggctgcctcatatgatgctatcaagagtgctatcaagtaagtatatagcttccaacgcaaggggaatgtacatctcattttgcgcactgttgctagaactgcatcttgtggcaggggataccgctcagtgatgtatgttactgaaacatacatgtgaaggattcctagaaaagtgtagttacgtgtgttggtgggcgcagaactgcacaagttatccttaagttagtagtgtgtccctgacgagaatatgctaattgttttacaggtctgcatcagagggaaagctcaagggaatcataggatatgttgaggaagacctggtttctactgactttgttggtgacagcaggtatgcctttttgtcttgagaggccctgtaagaaatctgtaatgcagatctgctccaaactaagtggttacggacgaactatctcctgtatgctatcattcattctctgtactcatctttgactcaggtcgagcatcttcgacgccaaggctggaattgctcttaacgataactttgtcaagcttgtcgcctggtacgacaacgagtggggttacaggtgagccacttgcagttcaaactattaaccatgtacaatactccatgcccaatttgctcttactgatctttcttttttgaactattttctgcagcaaccgtgtcatcgacctgatccgccacatggccaagacccagtagaatccttttgcttgccatggtattccatggccgccgagccggagataccggtatgctttgtctatgctgagaataaaacgtggacggtgttcatcaggacccaccccctctgttaatgctagttgggataatgagttgcattttgttttccaatctacctacttgtaagttgtaacgatgctgatgatatggacctgagtctacttttttgcttgtgaagaatataagccgtccagtgcagttgtaattttgttatgctggttgcatatatgggctttgtgtttggttcgtgctacctcttcacttctgcttgtttgtttggtcgtgtagggcaacgtctcatgatcagcttagtttgctctttcgtagttgctctcaatgtttattactccagaataacgtggcctttgcgattcagttgtgttgg</dnaseqindica> |
| External Link(s) |
- ↑ 1.0 1.1 1.2 1.3 1.4 Yueh-Chu Tien;Phimonphan Chuankhayan;Yen-Chieh Huang;Chung-De Chen;Jahan Alikhajeh;Shou-Lin Chang;Chun-Jung Chen. Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis. Plant Molecular Biology[J], 2012, 80(4-5): 389-403.
- ↑ 2.0 2.1 2.2 Pillai, M. A., et al.Molecular cloning, characterization, expression and chromosomal location of OsGAPDH, a submergence responsive gene in rice (Oryza sativa L.). Theoretical and Applied Genetics[J], 2002, 105(1): 34-42.
