Glycerol-1-phosphate dehydrogenase [NAD(P)+] - Methanobacterium thermoautotrophicum

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Reviewed, UniProtKB/Swiss-Prot P72010 (G1PDH_METTH)

Last modified January 19, 2010. Version 73. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Glycerol-1-phosphate dehydrogenase [NAD(P)+]
      Short name=G1P dehydrogenase
      Short name=G1PDH
    EC=1.1.1.261
Alternative name(s):
    sn-glycerol-1-phosphate dehydrogenase
    Enantiomeric glycerophosphate synthase

Gene names

Name:	egsA
Ordered Locus Names:	MTH_610

Organism

Methanobacterium thermoautotrophicum [Complete proteome] [HAMAP]

Taxonomic identifier

187420 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

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Protein attributes

Sequence length	347 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol-1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea. Is also able to catalyze the reverse reaction, i.e. the NAD(P)⁺-dependent oxidation of G1P but not of G3P. Is not active toward glycerol, dihydroxyacetone, glyceraldehyde-3-phosphate, glyceraldehyde and glycerol-2-phosphate. Ref.4 Ref.7
Catalytic activity	sn-glycerol-1-phosphate + NAD(P)⁺ = glycerone phosphate + NAD(P)H. Ref.4
Cofactor	Binds 1 zinc ion per subunit. Ref.7 Ref.6
Enzyme regulation	Partially inhibited by divalent metal cations such as Co²⁺, Cu²⁺ and Ni²⁺. Ref.4
Pathway	Membrane lipid metabolism; glycerophospholipid metabolism. HAMAP MF_00497
Subunit structure	Homooctamer. Ref.4
Subcellular location	Cytoplasm Potential HAMAP MF_00497.
Miscellaneous	G1PDH is a pro-R type dehydrogenase, which selectively transfers the pro-R hydrogen from NADH to dihydroxyacetonephosphate. HAMAP MF_00497
Sequence similarities	Belongs to the glycerol-1-phosphate dehydrogenase family.
Biophysicochemical properties	Kinetic parameters: K_M=2.17 mM for DHAP (in the presence of NADH as coenzyme) HAMAP MF_00497 K_M=0.58 mM for DHAP (in the presence of NADPH as coenzyme) K_M=0.129 mM for NADH K_M=0.025 mM for NADPH K_M=16.3 mM for G1P (in the presence of NAD as coenzyme) K_M=4.8 mM for G1P (in the presence of NADP as coenzyme) K_M=0.127 mM for NAD⁺ K_M=0.270 mM for NADP⁺ V_max=610 µmol/min/mg enzyme for DHAP reduction with NADH as coenzyme V_max=303 µmol/min/mg enzyme for DHAP reduction with NADPH as coenzyme V_max=39.8 µmol/min/mg enzyme for G1P oxidation with NADH as coenzyme V_max=23.9 µmol/min/mg enzyme for G1P oxidation with NADPH as coenzyme pH dependence: Optimum pH is 6.6-7-4. Activity decreases gradually at pH over 7.4 or below 6.6. Temperature dependence: Optimum temperature is 75 degrees Celsius.

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Ontologies

Keywords
Biological process	Phospholipid biosynthesis
Cellular component	Cytoplasm
Ligand	Metal-binding NAD NADP Zinc
Molecular function	Oxidoreductase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	aromatic amino acid family biosynthetic process Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW phospholipid biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3-dehydroquinate synthase activity Inferred from electronic annotation. Source: InterPro glycerol-1-phosphate dehydrogenase [NAD(P)+] activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 347

347

Glycerol-1-phosphate dehydrogenase [NAD(P)+] HAMAP MF_00497

PRO_0000157345

Regions

Nucleotide binding

94 – 98

NAD By similarity

Nucleotide binding

116 – 119

NAD By similarity

Sites

Metal binding

168

Zinc; catalytic Probable

Metal binding

248

Zinc; catalytic Probable

Metal binding

264

Zinc; catalytic Probable

Binding site

121

Substrate Probable

Binding site

125

NAD By similarity

Binding site

168

Substrate Probable

Binding site

252

Substrate Probable

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Sequences

Sequence

Length

Mass (Da)

Tools

P72010-1 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: 46D3600C30515413
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FASTA

347

36,963

        10         20         30         40         50         60 
MDPRKIQLPR EIYTGPGVIE DTGRICRDLR FEGRAMVVTG PRTLQIAGEA AIESLQAEGF 

        70         80         90        100        110        120 
EVDQVTVDDA TMASVRNVQD GLDGVSVVLG VGGGKVIDVA KMSATLEGLH FISVPTAASH 

       130        140        150        160        170        180 
DGIASPRASI RNGEGTASLE ASSPIGVIAD TEIISRAPFR LLASGCADII SNYTAIMDWK 

       190        200        210        220        230        240 
LAHRLLNERY SESAAALSLM TAKMIIKSAD AIKEGLEESA RLAVKSLISS GIAISIAGSS 

       250        260        270        280        290        300 
RPASGSEHKF SHALDMIAPK PALHGEQCGV GTIMMMHLHG GDWQFIRDAL ARINAPTTAA 

       310        320        330        340 
ELGIDPEYII EALTMAHNIR RERYTILGDR GLTREAAERL AKITEVI

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent." Koga Y., Kyuragi T., Nishihara M., Sone N. J. Mol. Evol. 46:54-63(1998) [PubMed: 9419225] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: Delta H.
[2]	Erratum Koga Y., Kyuragi T., Nishihara M., Sone N. J. Mol. Evol. 47:631-631(1998) [PubMed: 9797414] [Abstract]
[3]	"Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics." Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D., Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R. Reeve J.N. J. Bacteriol. 179:7135-7155(1997) [PubMed: 9371463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Delta H.
[4]	"Purification and properties of sn-glycerol-1-phosphate dehydrogenase from Methanobacterium thermoautotrophicum: characterization of the biosynthetic enzyme for the enantiomeric glycerophosphate backbone of ether polar lipids of Archaea." Nishihara M., Koga Y. J. Biochem. 122:572-576(1997) [PubMed: 9348086] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-23, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES. Strain: Delta H.
[5]	Erratum Nishihara M., Koga Y. J. Biochem. 123:194-194(1998)
[6]	"Analysis of membrane stereochemistry with homology modeling of sn-glycerol-1-phosphate dehydrogenase." Daiyasu H., Hiroike T., Koga Y., Toh H. Protein Eng. 15:987-995(2002) [PubMed: 12601138] [Abstract] Cited for: COFACTOR, 3D-STRUCTURE MODELING.
[7]	"Transfer of pro-R hydrogen from NADH to dihydroxyacetonephosphate by sn-glycerol-1-phosphate dehydrogenase from the archaeon Methanothermobacter thermautotrophicus." Koga Y., Sone N., Noguchi S., Morii H. Biosci. Biotechnol. Biochem. 67:1605-1608(2003) [PubMed: 12913312] [Abstract] Cited for: FUNCTION, COFACTOR, STEREOSPECIFICITY.

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Cross-references

Sequence databases
EMBL GenBank DDBJ	D88555 Genomic DNA. Translation: BAA13644.1. AE000666 Genomic DNA. Translation: AAB85116.1.
PIR	B69181.
RefSeq	NP_275753.1.
3D structure databases
SMR	P72010. Positions 4-347.
ModBase	Search...
Protein-protein interaction databases
STRING	P72010.
Genome annotation databases
GeneID	1470571.
GenomeReviews	Gene locus MTH_610 in contig AE000666_GR.
KEGG	mth:MTH610.
NMPDR	fig\|187420.1.peg.608.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	arNOG04488.
HOGENOM	HBG672951.
OMA	KWMQLPR.
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-14507. MTHE187420:MTH610-MONOMER.
BRENDA	1.1.1.261. 270.
Family and domain databases
HAMAP	MF_00497_A. G1P_dehydrogenase_A. [Tree]
InterPro	IPR002658. DHQ_synth_AroB. IPR016205. Glycerol_DH. [Graphical view]
Pfam	PF01761. DHQ_synthase. 1 hit. [Graphical view]
PIRSF	PIRSF000112. Glycerol_dehydrogenase. 1 hit.
ProtoNet	Search...

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Entry information

Entry name

G1PDH_METTH

Accession

Primary (citable) accession number: P72010

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 5, 2001
Last sequence update:	February 1, 1997
Last modified:	January 19, 2010
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents