Glycine dehydrogenase (decarboxylating): Difference between revisions
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| Name = glycine dehydrogenase (decarboxylating) |
| Name = glycine dehydrogenase (decarboxylating) |
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'''Glycine dehydrogenase [decarboxylating], mitochondrial''' also known as '''glycine cleavage system P protein''' or '''glycine decarboxylase''' is an [[enzyme]] that in humans is encoded by the ''GLDC'' [[gene]].<ref name="pmid1993704">{{cite journal | author = Kume A, Koyata H, Sakakibara T, Ishiguro Y, Kure S, Hiraga K | title = The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures | journal = J Biol Chem | volume = 266 | issue = 5 | pages = 3323–9 | year = 1991 | month = Mar | pmid = 1993704 | pmc = | doi = }}</ref><ref name="pmid1996985">{{cite journal | author = Kure S, Narisawa K, Tada K | title = Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia | journal = Biochem Biophys Res Commun | volume = 174 | issue = 3 | pages = 1176–82 | year = 1991 | month = Mar | pmid = 1996985 | pmc = | doi =10.1016/0006-291X(91)91545-N }}</ref><ref name="entrez">{{cite web | title = Entrez Gene: GLDC glycine dehydrogenase (decarboxylating)| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2731| accessdate = }}</ref> |
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== Reaction == |
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:glycine + H-protein-lipoyllysine <math>\rightleftharpoons</math> H-protein-S-aminomethyldihydrolipoyllysine + CO<sub>2</sub> |
:glycine + H-protein-lipoyllysine <math>\rightleftharpoons</math> H-protein-S-aminomethyldihydrolipoyllysine + CO<sub>2</sub> |
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Thus, the two [[substrate (biochemistry)|substrates]] of this enzyme are [[glycine]] and [[H-protein-lipoyllysine]], whereas its two [[product (chemistry)|products]] are [[H-protein-S-aminomethyldihydrolipoyllysine]] and [[carbon dioxide|CO<sub>2</sub>]]. |
Thus, the two [[substrate (biochemistry)|substrates]] of this enzyme are [[glycine]] and [[H-protein-lipoyllysine]], whereas its two [[product (chemistry)|products]] are [[H-protein-S-aminomethyldihydrolipoyllysine]] and [[carbon dioxide|CO<sub>2</sub>]]. |
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This enzyme belongs to the family of [[oxidoreductase]]s, specifically those acting on the CH-NH2 group of donors with a disulfide as acceptor. |
This enzyme belongs to the family of [[oxidoreductase]]s, specifically those acting on the CH-NH2 group of donors with a disulfide as acceptor. This enzyme participates in [[glycine, serine and threonine metabolism]]. It employs one [[cofactor (biochemistry)|cofactor]], [[pyridoxal phosphate]]. |
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== |
== Function == |
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Glycine decarboxylase is a P-protein of the [[glycine cleavage system]] in [[eukaryotes]]. The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its [[pyridoxal phosphate]] cofactor. Carbon dioxide is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. |
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As of late 2007, 5 [[tertiary structure|structures]] have been solved for this class of enzymes, with [[Protein Data Bank|PDB]] accession codes {{PDB link|1HPC}}, {{PDB link|1HTP}}, {{PDB link|1WYT}}, {{PDB link|1WYU}}, and {{PDB link|1WYV}}. |
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Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase).<ref name="entrez"/> |
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== Clinical significance == |
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[[D-Glyceric acidemia|Glycine encephalopathy]] may be due to a defect in any one of these enzymes.<ref name="entrez">{{cite web | title = Entrez Gene: GLDC glycine dehydrogenase (decarboxylating)| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2731| accessdate = }}</ref> |
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==References== |
==References== |
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{{reflist |
{{reflist}} |
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==Further reading== |
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{{refbegin | 2}} |
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* {{cite journal | author = Hiraga K, Kikuchi G | date = 1980 | title = The mitochondrial glycine cleavage system. Functional association of glycine decarboxylase and aminomethyl carrier protein | journal = J. Biol. Chem. | volume = 255 | pages = 11671–6 | pmid = 7440563 | issue = 24 }} |
* {{cite journal | author = Hiraga K, Kikuchi G | date = 1980 | title = The mitochondrial glycine cleavage system. Functional association of glycine decarboxylase and aminomethyl carrier protein | journal = J. Biol. Chem. | volume = 255 | pages = 11671–6 | pmid = 7440563 | issue = 24 }} |
||
* {{cite journal | author = Perham RN | date = 2000 | title = Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions | journal = Annu. Rev. Biochem. | volume = 69 | pages = 961–1004 | pmid = 10966480 | doi = 10.1146/annurev.biochem.69.1.961 }} |
* {{cite journal | author = Perham RN | date = 2000 | title = Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions | journal = Annu. Rev. Biochem. | volume = 69 | pages = 961–1004 | pmid = 10966480 | doi = 10.1146/annurev.biochem.69.1.961 }} |
||
* {{cite journal | author = Broadwater JA, Haas JA, Fox BG, Booker SJ | date = 2005 | title = Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase | journal = Protein. Expr. Purif. | volume = 39 | pages = 269–82 | pmid = 15642479 | issue = 2 | doi = 10.1016/j.pep.2004.10.021 }} |
* {{cite journal | author = Broadwater JA, Haas JA, Fox BG, Booker SJ | date = 2005 | title = Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase | journal = Protein. Expr. Purif. | volume = 39 | pages = 269–82 | pmid = 15642479 | issue = 2 | doi = 10.1016/j.pep.2004.10.021 }}*{{cite journal | author=Applegarth DA, Toone JR |title=Nonketotic hyperglycinemia (glycine encephalopathy): laboratory diagnosis. |journal=Mol. Genet. Metab. |volume=74 |issue= 1-2 |pages= 139–46 |year= 2001 |pmid= 11592811 |doi= 10.1006/mgme.2001.3224 }} |
||
*{{cite journal | author=Kure S, Takayanagi M, Narisawa K, ''et al.'' |title=Identification of a common mutation in Finnish patients with nonketotic hyperglycinemia. |journal=J. Clin. Invest. |volume=90 |issue= 1 |pages= 160–4 |year= 1992 |pmid= 1634607 |doi=10.1172/JCI115831 | pmc=443076 }} |
|||
*{{cite journal | author=Sakakibara T, Koyata H, Ishiguro Y, ''et al.'' |title=One of the two genomic copies of the glycine decarboxylase cDNA has been deleted at a 5' region in a patient with nonketotic hyperglycinemia. |journal=Biochem. Biophys. Res. Commun. |volume=173 |issue= 3 |pages= 801–6 |year= 1991 |pmid= 2268343 |doi=10.1016/S0006-291X(05)80858-7 }} |
|||
*{{cite journal | author=Burton BK, Pettenati MJ, Block SM, ''et al.'' |title=Nonketotic hyperglycinemia in a patient with the 9p- syndrome. |journal=Am. J. Med. Genet. |volume=32 |issue= 4 |pages= 504–5 |year= 1989 |pmid= 2773994 |doi= 10.1002/ajmg.1320320416 }} |
|||
*{{cite journal | author=Hayasaka K, Kochi H, Hiraga K, Kikuchi G |title=Purification and properties of glycine decarboxylase, a component of the glycine cleavage system, from rat liver mitochondria and immunochemical comparison of this enzyme from various sources. |journal=J. Biochem. |volume=88 |issue= 4 |pages= 1193–9 |year= 1981 |pmid= 6778858 |doi= }} |
|||
*{{cite journal | author=Hiraga K, Kochi H, Hayasaka K, ''et al.'' |title=Defective glycine cleavage system in nonketotic hyperglycinemia. Occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein. |journal=J. Clin. Invest. |volume=68 |issue= 2 |pages= 525–34 |year= 1981 |pmid= 6790577 |doi=10.1172/JCI110284 | pmc=370827 }} |
|||
*{{cite journal | author=Takayanagi M, Kure S, Sakata Y, ''et al.'' |title=Human glycine decarboxylase gene (GLDC) and its highly conserved processed pseudogene (psiGLDC): their structure and expression, and the identification of a large deletion in a family with nonketotic hyperglycinemia. |journal=Hum. Genet. |volume=106 |issue= 3 |pages= 298–305 |year= 2000 |pmid= 10798358 |doi=10.1007/s004390051041 }} |
|||
*{{cite journal | author=Toone JR, Applegarth DA, Coulter-Mackie MB, James ER |title=Biochemical and molecular investigations of patients with nonketotic hyperglycinemia. |journal=Mol. Genet. Metab. |volume=70 |issue= 2 |pages= 116–21 |year= 2000 |pmid= 10873393 |doi= 10.1006/mgme.2000.3000 }} |
|||
*{{cite journal | author=Toone JR, Applegarth DA, Coulter-Mackie MB, James ER |title=Recurrent mutations in P- and T-proteins of the glycine cleavage complex and a novel T-protein mutation (N145I): a strategy for the molecular investigation of patients with nonketotic hyperglycinemia (NKH). |journal=Mol. Genet. Metab. |volume=72 |issue= 4 |pages= 322–5 |year= 2001 |pmid= 11286506 |doi= 10.1006/mgme.2001.3158 }} |
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*{{cite journal | author=Kure S, Kojima K, Ichinohe A, ''et al.'' |title=Heterozygous GLDC and GCSH gene mutations in transient neonatal hyperglycinemia. |journal=Ann. Neurol. |volume=52 |issue= 5 |pages= 643–6 |year= 2002 |pmid= 12402263 |doi= 10.1002/ana.10367 }} |
|||
*{{cite journal | author=Strausberg RL, Feingold EA, Grouse LH, ''et al.'' |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899–903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 | pmc=139241 }} |
|||
*{{cite journal | author=Toone JR, Applegarth DA, Laliberte G |title=Gene Symbol: GLDC. Disease: NKH glycine encephalopathy. |journal=Hum. Genet. |volume=113 |issue= 5 |pages= 465 |year= 2003 |pmid= 14552331 |doi=10.1007/s00439-003-1014-5 }} |
|||
*{{cite journal | author=Dinopoulos A, Kure S, Chuck G, ''et al.'' |title=Glycine decarboxylase mutations: a distinctive phenotype of nonketotic hyperglycinemia in adults. |journal=Neurology |volume=64 |issue= 7 |pages= 1255–7 |year= 2006 |pmid= 15824356 |doi= 10.1212/01.WNL.0000156800.23776.40 }} |
|||
*{{cite journal | author=Flusser H, Korman SH, Sato K, ''et al.'' |title=Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. |journal=Neurology |volume=64 |issue= 8 |pages= 1426–30 |year= 2006 |pmid= 15851735 |doi= 10.1212/01.WNL.0000158475.12907.D6 }} |
|||
*{{cite journal | author=Boneh A, Korman SH, Sato K, ''et al.'' |title=A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among patients with glycine encephalopathy in Jerusalem. |journal=J. Hum. Genet. |volume=50 |issue= 5 |pages= 230–4 |year= 2005 |pmid= 15864413 |doi= 10.1007/s10038-005-0243-y }} |
|||
*{{cite journal | author=Kimura K, Wakamatsu A, Suzuki Y, ''et al.'' |title=Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. |journal=Genome Res. |volume=16 |issue= 1 |pages= 55–65 |year= 2006 |pmid= 16344560 |doi= 10.1101/gr.4039406 | pmc=1356129 }} |
|||
*{{cite journal | author=Korman SH, Wexler ID, Gutman A, ''et al.'' |title=Treatment from birth of nonketotic hyperglycinemia due to a novel GLDC mutation. |journal=Ann. Neurol. |volume=59 |issue= 2 |pages= 411–5 |year= 2006 |pmid= 16404748 |doi= 10.1002/ana.20759 }} |
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}} |
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{{refend}} |
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{{1.4-enzyme-stub}} |
{{1.4-enzyme-stub}} |
Revision as of 19:50, 20 October 2010
Template:Fix bunching Template:PBB Template:Fix bunching
glycine dehydrogenase (decarboxylating) | |||||||||
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Identifiers | |||||||||
EC no. | 1.4.4.2 | ||||||||
CAS no. | 37259-67-9 | ||||||||
Databases | |||||||||
IntEnz | IntEnz view | ||||||||
BRENDA | BRENDA entry | ||||||||
ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
|
Template:Fix bunching Glycine dehydrogenase [decarboxylating], mitochondrial also known as glycine cleavage system P protein or glycine decarboxylase is an enzyme that in humans is encoded by the GLDC gene.[1][2][3]
Reaction
Glycine dehydrogenase (decarboxylating) (EC 1.4.4.2) is an enzyme that catalyzes the following chemical reaction:
- glycine + H-protein-lipoyllysine H-protein-S-aminomethyldihydrolipoyllysine + CO2
Thus, the two substrates of this enzyme are glycine and H-protein-lipoyllysine, whereas its two products are H-protein-S-aminomethyldihydrolipoyllysine and CO2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-NH2 group of donors with a disulfide as acceptor. This enzyme participates in glycine, serine and threonine metabolism. It employs one cofactor, pyridoxal phosphate.
Function
Glycine decarboxylase is a P-protein of the glycine cleavage system in eukaryotes. The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor. Carbon dioxide is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein.
Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase).[3]
Clinical significance
Glycine encephalopathy may be due to a defect in any one of these enzymes.[3]
References
- ^ Kume A, Koyata H, Sakakibara T, Ishiguro Y, Kure S, Hiraga K (1991). "The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures". J Biol Chem. 266 (5): 3323–9. PMID 1993704.
{{cite journal}}
: Unknown parameter|month=
ignored (help)CS1 maint: multiple names: authors list (link) - ^ Kure S, Narisawa K, Tada K (1991). "Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia". Biochem Biophys Res Commun. 174 (3): 1176–82. doi:10.1016/0006-291X(91)91545-N. PMID 1996985.
{{cite journal}}
: Unknown parameter|month=
ignored (help)CS1 maint: multiple names: authors list (link) - ^ a b c "Entrez Gene: GLDC glycine dehydrogenase (decarboxylating)".
Further reading
- Hiraga K, Kikuchi G (1980). "The mitochondrial glycine cleavage system. Functional association of glycine decarboxylase and aminomethyl carrier protein". J. Biol. Chem. 255 (24): 11671–6. PMID 7440563.
- Perham RN (2000). "Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions". Annu. Rev. Biochem. 69: 961–1004. doi:10.1146/annurev.biochem.69.1.961. PMID 10966480.
- Broadwater JA, Haas JA, Fox BG, Booker SJ (2005). "Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase". Protein. Expr. Purif. 39 (2): 269–82. doi:10.1016/j.pep.2004.10.021. PMID 15642479.
{{cite journal}}
: CS1 maint: multiple names: authors list (link)*Applegarth DA, Toone JR (2001). "Nonketotic hyperglycinemia (glycine encephalopathy): laboratory diagnosis". Mol. Genet. Metab. 74 (1–2): 139–46. doi:10.1006/mgme.2001.3224. PMID 11592811. - Kure S, Takayanagi M, Narisawa K; et al. (1992). "Identification of a common mutation in Finnish patients with nonketotic hyperglycinemia". J. Clin. Invest. 90 (1): 160–4. doi:10.1172/JCI115831. PMC 443076. PMID 1634607.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Sakakibara T, Koyata H, Ishiguro Y; et al. (1991). "One of the two genomic copies of the glycine decarboxylase cDNA has been deleted at a 5' region in a patient with nonketotic hyperglycinemia". Biochem. Biophys. Res. Commun. 173 (3): 801–6. doi:10.1016/S0006-291X(05)80858-7. PMID 2268343.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Burton BK, Pettenati MJ, Block SM; et al. (1989). "Nonketotic hyperglycinemia in a patient with the 9p- syndrome". Am. J. Med. Genet. 32 (4): 504–5. doi:10.1002/ajmg.1320320416. PMID 2773994.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Hayasaka K, Kochi H, Hiraga K, Kikuchi G (1981). "Purification and properties of glycine decarboxylase, a component of the glycine cleavage system, from rat liver mitochondria and immunochemical comparison of this enzyme from various sources". J. Biochem. 88 (4): 1193–9. PMID 6778858.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - Hiraga K, Kochi H, Hayasaka K; et al. (1981). "Defective glycine cleavage system in nonketotic hyperglycinemia. Occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein". J. Clin. Invest. 68 (2): 525–34. doi:10.1172/JCI110284. PMC 370827. PMID 6790577.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Takayanagi M, Kure S, Sakata Y; et al. (2000). "Human glycine decarboxylase gene (GLDC) and its highly conserved processed pseudogene (psiGLDC): their structure and expression, and the identification of a large deletion in a family with nonketotic hyperglycinemia". Hum. Genet. 106 (3): 298–305. doi:10.1007/s004390051041. PMID 10798358.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Toone JR, Applegarth DA, Coulter-Mackie MB, James ER (2000). "Biochemical and molecular investigations of patients with nonketotic hyperglycinemia". Mol. Genet. Metab. 70 (2): 116–21. doi:10.1006/mgme.2000.3000. PMID 10873393.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - Toone JR, Applegarth DA, Coulter-Mackie MB, James ER (2001). "Recurrent mutations in P- and T-proteins of the glycine cleavage complex and a novel T-protein mutation (N145I): a strategy for the molecular investigation of patients with nonketotic hyperglycinemia (NKH)". Mol. Genet. Metab. 72 (4): 322–5. doi:10.1006/mgme.2001.3158. PMID 11286506.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - Kure S, Kojima K, Ichinohe A; et al. (2002). "Heterozygous GLDC and GCSH gene mutations in transient neonatal hyperglycinemia". Ann. Neurol. 52 (5): 643–6. doi:10.1002/ana.10367. PMID 12402263.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Strausberg RL, Feingold EA, Grouse LH; et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Toone JR, Applegarth DA, Laliberte G (2003). "Gene Symbol: GLDC. Disease: NKH glycine encephalopathy". Hum. Genet. 113 (5): 465. doi:10.1007/s00439-003-1014-5. PMID 14552331.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - Dinopoulos A, Kure S, Chuck G; et al. (2006). "Glycine decarboxylase mutations: a distinctive phenotype of nonketotic hyperglycinemia in adults". Neurology. 64 (7): 1255–7. doi:10.1212/01.WNL.0000156800.23776.40. PMID 15824356.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Flusser H, Korman SH, Sato K; et al. (2006). "Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation". Neurology. 64 (8): 1426–30. doi:10.1212/01.WNL.0000158475.12907.D6. PMID 15851735.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Boneh A, Korman SH, Sato K; et al. (2005). "A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among patients with glycine encephalopathy in Jerusalem". J. Hum. Genet. 50 (5): 230–4. doi:10.1007/s10038-005-0243-y. PMID 15864413.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Kimura K, Wakamatsu A, Suzuki Y; et al. (2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC 1356129. PMID 16344560.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link) - Korman SH, Wexler ID, Gutman A; et al. (2006). "Treatment from birth of nonketotic hyperglycinemia due to a novel GLDC mutation". Ann. Neurol. 59 (2): 411–5. doi:10.1002/ana.20759. PMID 16404748.
{{cite journal}}
: Explicit use of et al. in:|author=
(help)CS1 maint: multiple names: authors list (link)
}}