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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0465.2 IGR0467 IGR0465.3 IGR0469 IGR0465.1 IGR0468 IGR0466 NG0563 aceF, - NG0564 lpdA,dldH, - NG0562 aceE, - NG0565 NG0560 fcuA, - NG0560.1 NG0560.2 NG0561 NG0563 aceF, - NG0564 lpdA,dldH, - NG0562 aceE, - NG0565 NG0560 fcuA, - NG0560.1 NG0560.2 NG0561 Type: tandem, Name:  - 29 NG0563 aceF, - NG0564 lpdA,dldH, - NG0562 aceE, - NG0565 fcuA, - NG0560.1 NG0560.2 NG0561 NG0560
* Calculated from Protein Sequence

Gene ID: NG0562

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
lpdA  dldH  

Definition:
dihydrolipoamide dehydrogenase (pyruvate dehydrogenase, E3 component, lipoamide dehydrogenase) (glycine cleavage system L protein)

Gene Start:
543889

Gene Stop:
542108

Gene Length:
1782

Molecular Weight*:
61785

pI*:
5.00

Net Charge*:
-17.43

EC:
1.8.1.4  

Functional Class:
Central intermediary metabolism; Glycine cleavage system  
Energy metabolism; Pyruvate dehydrogenase  

Pathway: pathway table
Citrate cycle (TCA cycle)
Glycine, serine and threonine metabolism
Glycolysis / Gluconeogenesis
Pyruvate metabolism

Secondary Evidence:
Hein,S. and Steinbuchel,A.
Biochemical and molecular characterization of the Alcaligenes eutrophus pyruvate dehydrogenase complex and identification of a new type of dihydrolipoamide dehydrogenase.
J. Bacteriol. 176 (14), 4394-4408 (1994)
Medline: 94292470.

Stephens,P.E., Lewis,H.M., Darlison,M.G. and Guest,J.R.
Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K12.
Eur. J. Biochem. 135 (3), 519-527 (1983)
Medline: 84004369

Steiert,P.S., Stauffer,L.T. and Stauffer,G.V.
The lpd gene product functions as the L protein in the Escherichia coli glycine cleavage enzyme system.
J. Bacteriol. 172 (10), 6142-6144 (1990)
Medline: 91008999.

Comment:
For other elements of the glycine cleavge system, see NG1325, NG1404, NG1406.


From GenBANK (gi:118673): In Vibrio cholera, the branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO2. It contains multiple copies of 3 enzymatic components: E1, E2, and E3. It catalyzes the reaction: dihydrolipoamide + NAD(+) = lipoamide + NADH, with FAD as a cofactor. The active site is a redox-active disulfide bond. It is also a component of the glycine cleavage system.

From Medline (9429247): The A. eutrophus pyruvate dehydrogenase complex, pdhA, pdhB, and pdhL encodes the pyruvate dehydrogenase (E1), the dihydrolipoamide acetyltransferase (E2), and the dihydrolipoamide dehydrogenase (E3) components, respectively. These genes occur colinearly in one gene cluster in the order pdhA, pdhB, ORF3, and pdhL. Microsequencing of the purified E3 component revealed an amino acid sequence which corresponded to the N-terminal amino acid sequence deduced from the nucleotide sequence of pdhL. The N-terminal region of PdhL comprising amino acids 1 to 112 was distinguished from all other known dihydrolipoamide dehydrogenases. It resembled the N terminus of dihydrolipoamide acyltransferases, and it contained one single lipoyl domain which was separated by an adjacent hinge region from the C-terminal region of the protein that exhibited high homology to classical dihydrolipoamide dehydrogenases.

From Medline (91008999): The lpd-encoded lipoamide dehydrogenase, common to the pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes, also functions as the lipoamide dehydrogenase (L protein) in the E.coli glycine cleavage enzyme complex. lpd allows the organism to use glycine as a serine source.

See also: E1, NG0565, and E2, NG0564.

Oklahoma ID: NGO.562c

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST; e.g. residues 1-594 are 66% similar to gb|AAA21600.1| (U09865) dihydrolipoamide dehydrogenase of Ralstonia eutropha.

Residues 1-594 are 97% similar to X81450, outer membrane protein P64k or PM-6, and are 99% similar to NMB1344, dihydrolipoamide dehydrogenase (pyruvate dehydrogenase, E3 component, lipoamide dehydrogenase), in N.meningitidis. Also similar to many other outer membrane proteins and dehydrogenases in N.meningitidis.

COGS Summary:  COGS Search
BeTs to 11 clades of COG1249
COG name: Dihydrolipoamide dehydrogenase/glutathione oxidoreductase and related enzymes
Functional Class:  C
The phylogenetic pattern of COG1249 is amt-YqvCEBRH--gp--inX
Number of proteins in this genome belonging to this COG is 3

Blocks Summary:  Blocks Search
***** PR00368 (FAD-dependent pyridine nucleotide reductase signature) with a combined E-value of 2.4e-32.
    PR00368A    119-141
    PR00368B    263-272
    PR00368C    298-323
    PR00368D    387-401
    PR00368E    430-437
***** IPB003016 (2-oxo acid dehydrogenases acyltransferase component lipoyl binding site) with a combined E-value of 2.3e-17.
    IPB003016    25-59
***** IPB000103 (Pyridine nucleotide-disulphide oxidoreductase class-II) with a combined E-value of 5.1e-16.
    IPB000103A    119-139
    IPB000103D    388-399
    IPB000103E    425-462
***** IPB001078 (2-Oxo acid dehydrogenase acyltransferase catalytic domain) with a combined E-value of 1.2e-13.
    IPB001078A    22-54
    IPB001078A    59-91
***** IPB001100 (Pyridine nucleotide-disulphide oxidoreductase, class I) with a combined E-value of 2.9e-10.
    IPB001100    153-167
***** IPB000171 (Bacterial-type phytoene dehydrogenase) with a combined E-value of 4.4e-07.
    IPB000171A    121-151
    IPB000171A    300-330


ProDom Summary:  Protein Domain Search
Residues 19-75 are 98% similar to a (BIOTIN DIHYDROLIPOAMIDE PYRUVATE DEHYDROGENASE) protein domain (PD000268) which is seen in Q51225_NEIME.

Residues 4-76 are 56% similar to a (PROTEIN REPEAT PRECURSOR DNA-BINDING NUCLEAR SIGNAL) protein domain (PD000540) which is seen in ODP2_ALCEU.



Paralogs:  Local Blast Search


NG0562 is paralogously related to NG0915 (dihydrolipoamide dehydrogenase E3 component) (8e-89), NG0564 (dihydrolipoamide S-acetyltransferase complex (E2 component of pyruvate dehydrogenase complex)) (8e-40), NG0925 (dihydrolipoamide dehydrogenase (E3 component of the pyruvate complex)) (3e-30) and NG0916 (dihydrolipoamide succinyltransferase E2 component) (2e-10).


Pfam Summary:  Pfam Search
Residues 4 to 76 (E-value = 9.7e-21) place NG0562 in the Biotin_lipoyl family which is described as Biotin-requiring enzyme (PF00364)
Residues 119 to 445 (E-value = 1.8e-93) place NG0562 in the Pyr_redox family which is described as Pyridine nucleotide-disulphide oxidoreductase (PF00070)
Residues 469 to 578 (E-value = 1.6e-49) place NG0562 in the Pyr_redox_dim family which is described as Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain (PF02852)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
1  
168
transmembrane  
299  
315

PDB Hit:
pdb|1OJT|1OJT STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE 883.0 0.000000
pdb|1BHY|1BHY LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF 879.0 0.000000
pdb|1EBD|1EBD-A DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH 324.0 2e-89
pdb|3LAD|3LAD-A

Gene Protein Sequence:
MALVELKVPDIGGHENVDIIAVEVNVGDTIAVDDTLITLETDKATMDVPA
EVAGVIKEVKVKVGDKISEGGLIVVVEAEGAAAAPKAEAAAAPAQEAPKA
AAPAPQAAQFGGAADAEYDVVVLGGGPGGYSAAFAAADEGLKVAIVERYK
TLGGVCLNVGCIPSKALLHNAAVIDEVRHLAANGIKYPKPELDIDMLRAY
KDGVVSRLTGGLAGMAKSRKVDVIQGDGQFLDPHHLEVSLTAGDAYEQAA
PTGEKKIVAFKNCIIAAGSRVTKLPFIPEDPRIIDSSGALALKEVPGKLL
IIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYR
FDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGK
LISAEKAGVAVTDRGFIEVDKQMRTNVPHIYAIGDIVGQPMLAHKAVHEG
HVAAENCAGHKAYFDARVIPGVAYTSPEVAWVGETELSAKASGRKITKAN
FPWAASGRAIANGCDNGFTKLIFDAETGRIIGGGIVGPNGGDMIGEVCLA
IEMGCDAADIGKTIHPHPTLGESIGMAAEVALGVCTDLPPQKKK

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCTTTAGTTGAATTGAAAGTGCCCGACATTGGCGGACACGAAAATGT
AGATATTATCGCGGTTGAAGTGAACGTTGGCGACACCATCGCCGTTGACG
ACACCCTGATTACCTTGGAAACCGACAAAGCGACGATGGACGTGCCTGCC
GAAGTTGCGGGCGTGATCAAAGAAGTGAAAGTCAAAGTCGGCGACAAAAT
CTCCGAAGGCGGTTTGATTGTCGTCGTCGAAGCCGAAGGTGCGGCTGCCG
CCCCTAAAGCCGAAGCGGCTGCCGCCCCGGCGCAAGAAGCACCCAAAGCT
GCCGCTCCTGCTCCGCAAGCCGCGCAATTCGGCGGTGCTGCCGATGCCGA
GTACGACGTGGTCGTATTGGGCGGCGGTCCCGGCGGTTACTCCGCTGCAT
TTGCCGCTGCCGATGAAGGCTTGAAAGTCGCCATCGTCGAGCGTTACAAA
ACTTTGGGCGGCGTTTGCCTGAACGTCGGCTGTATCCCTTCCAAAGCCTT
GTTGCACAATGCCGCCGTTATCGACGAAGTGCGCCACTTGGCTGCCAACG
GTATCAAATACCCCAAGCCGGAACTCGACATCGATATGCTTCGCGCCTAC
AAAGACGGCGTGGTTTCCCGCCTCACGGGTGGTTTGGCAGGTATGGCGAA
AAGCCGTAAAGTGGACGTTATCCAAGGCGACGGGCAATTCTTGGATCCTC
ACCACTTGGAAGTGTCGCTGACTGCCGGCGACGCGTACGAACAGGCAGCC
CCTACCGGCGAGAAAAAAATCGTTGCCTTCAAAAACTGTATCATTGCAGC
AGGCAGCCGCGTAACCAAACTGCCTTTCATTCCTGAAGATCCGCGCATCA
TCGATTCCAGCGGCGCACTGGCACTGAAAGAAGTACCGGGCAAACTGCTG
ATTATCGGCGGCGGCATTATCGGCCTCGAGATGGGTACGGTTTACAGCAC
GCTGGGTTCTCGCCTGGATGTGGTTGAAATGATGGACGGCCTGATGCAAG
GCGCAGACCGCGACTTGGTTAAAGTATGGCAAAAACAAAACGAATACCGT
TTTGACAACATTATGGTCAACACCAAAACCGTTGCAGTCGAGCCGAAAGA
AGACGGCGTTTACGTTACCTTTGAAGGTGCAAATGCACCTAAAGAGCCGC
AACGTTACGATGCCGTACTGGTCGCGGCAGGCCGTGCGCCTAACGGCAAA
CTCATCAGCGCAGAAAAAGCCGGTGTTGCCGTTACCGATCGTGGCTTCAT
CGAAGTTGACAAACAAATGCGCACCAACGTACCGCACATCTACGCTATCG
GCGATATCGTCGGTCAACCGATGTTGGCACACAAAGCCGTTCACGAAGGC
CACGTTGCCGCTGAAAACTGTGCCGGCCACAAAGCCTACTTCGACGCACG
CGTTATTCCCGGCGTTGCCTACACTTCCCCCGAAGTGGCATGGGTCGGTG
AAACCGAATTGTCTGCCAAAGCATCAGGCCGCAAAATTACCAAAGCCAAC
TTCCCATGGGCGGCTTCCGGTCGTGCGATTGCCAACGGTTGCGACAACGG
CTTTACCAAGCTGATTTTCGATGCCGAAACCGGCCGCATCATCGGCGGCG
GCATTGTCGGTCCGAACGGTGGCGACATGATCGGCGAAGTCTGCCTTGCC
ATCGAAATGGGCTGCGACGCGGCAGACATCGGCAAAACCATCCACCCGCA
CCCGACCTTGGGCGAATCCATCGGTATGGCTGCGGAAGTGGCTTTGGGTG
TATGTACCGACCTGCCTCCTCAAAAGAAAAAA


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