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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0754 IGR0756 IGR0757 IGR0758 IGR0761 IGR0759 IGR0756.1 IGR0753 IGR0755 IGR0760 IGR0756.2 fitA, - NG0908 NG0914 fitB, - NG0907 NG0910 tpn, - NG0909 sucD, - NG0912 sucC, - NG0913 sucB, - NG0916 dldH, - NG0915 NG0911 NG0906 fitA, - NG0908 NG0914 fitB, - NG0907 NG0910 tpn, - NG0909 sucD, - NG0912 sucC, - NG0913 sucB, - NG0916 dldH, - NG0915 NG0911 NG0906 Type: direct, Name:  - 117 NG0914 fitB, - NG0907 NG0910 tpn, - NG0909 sucD, - NG0912 sucC, - NG0913 sucB, - NG0916 dldH, - NG0915 fitA, - NG0908 NG0911 NG0906
* Calculated from Protein Sequence

Gene ID: NG0912

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
sucD  

Definition:
succinyl-CoA synthetase, alpha subunit

Gene Start:
891519

Gene Stop:
890632

Gene Length:
888

Molecular Weight*:
30536

pI*:
5.70

Net Charge*:
-3.93

EC:
6.2.1.5  

Functional Class:
Energy metabolism; TCA cycle  

Pathway: pathway table
C5-Branched dibasic acid metabolism
Citrate cycle (TCA cycle)
Propanoate metabolism
Reductive carboxylate cycle (CO2 fixation)

Secondary Evidence:
Fraser,M.E., James,M.N., Bridger,W.A. and Wolodko,W.T. A detailed structural description of Escherichia coli succinyl-CoA synthetase. J. Mol. Biol. 285 (4): 1633-1653 (1999) [Medline: 99141407].

Joyce,M.A., Fraser,M.E., James,M.N., Bridger,W.A. and Wolodko,W.T. ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography. Biochemistry 39 (1): 17-25 (2000) [Medline: 20092606].

Freestone,P., Grant,S., Toth,I. and Norris,V. Identification of phosphoproteins in Escherichia coli . Mol. Microbiol. 15 (3): 573-580 (1995) [Medline: 95302968].

Buck,D. and Guest,J.R. Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon. Biochem. J. 260 (3): 737-747 (1989) [Medline: 89350876].

Buck,D., Spencer,M.E. and Guest,J.R. Primary structure of the succinyl-CoA synthetase of Escherichia coli. Biochemistry 24 (22): 6245-6252 (1985) [Medline: 86104124].

Comment:
From GenBANK (gi:135028): The catalytic activity of this enzyme is: succinate + CoA + ATP = succinyl-CoA + ADP + orthophosphate. It exhibits two interesting properties: 'substrate synergism', in which the enzyme is most active for the catalysis of its partial reactions only when all the substrate binding sites are occupied, and 'catalytic cooperativity' between alternating active sites in the tetramer, whereby the interaction of substrates (particularly ATP) at one site is needed to promote catalysis at the other. In E. coli, this tetramer of two alpha and two beta chains catalyzes its reaction via 3 steps that involve phosphoryl enzyme and enzyme-bound succinyl phosphate as intermediates. During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP & thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. The succinyl-CoA synthetases of eukaryotes and gram-positive bacteria differ from the gram-negative enzymes in containing single alpha-beta dimers. It also exhibits similarity to other alpha subunits of succinyl-CoA synthetase, of malate-CoA ligase and to ATP citrate-lyase.

See also the beta subunit, NG0913.

Oklahoma ID: NGO.912c

Blast Summary:  PSI-Blast Search
NG0912 is orthologous to AE002447, N. meningitidis MC58 succinyl-CoA synthetase, alpha subunit : residues 1-296 have similarity to residues 1-296 in NG0912.
NG0912 has very strong hits to succinyl-CoA synthase proteins in several organisms outside of Neisseria.

COGS Summary:  COGS Search
BeTs to 11 clades of COG0074
COG name: Succinyl-CoA synthetase, alpha subunit
Functional Class:  C
The phylogenetic pattern of COG0074 is Amt-yQ-cEbrh------inx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000303 (ATP-citrate lyase/succinyl-CoA ligases) with a combined E-value of 7.9e-70.
    IPB000303A    23-69
    IPB000303B    92-101
    IPB000303C    121-164
    IPB000303D    230-253
    IPB000303A    5-51
***** IPB003781 (DUF184) with a combined E-value of 2.4e-28.
    IPB003781A    121-130
    IPB003781B    154-182
    IPB003781C    192-211
    IPB003781D    244-271
    IPB003781D    259-286


ProDom Summary:  Protein Domain Search
Residues 133-250 are 64% similar to a (LIGASE SUCCINYL-COA ALPHA SYNTHETASE) protein domain (PD002034) which is seen in SUCD_ECOLI.

Residues 18-132 are 58% similar to a (PROTEIN LIGASE SUCCINYL-COA ALPHA) protein domain (PD001432) which is seen in SUCD_COXBU.



Paralogs:  Local Blast Search


NG0912 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 4 to 115 (E-value = 6.6e-68) place NG0912 in the CoA_binding family which is described as CoA binding domain (PF02629)
Residues 135 to 276 (E-value = 4.1e-57) place NG0912 in the Ligase_CoA family which is described as CoA-ligase (PF00549)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
53  
296
transmembrane  
81  
97

PDB Hit:
pdb|1JLL|1JLL-A CRYSTAL 352.0 4e-98
pdb|1CQI|1CQI-A CRYSTAL STRUCTURE OF THE COMPLEX OF ADP AND MG2+349.0 5e-97
pdb|2SCU|2SCU-A A DETAILED DESCRIPTION OF THE STRUCTURE OF 349.0 5e-97
pdb|1EUC|1EUC-A CRYSTAL STRUCTURE OF DEPHOSPHORYLATED

Gene Protein Sequence:
MSVLINKDTKVLVQGFTGKNGTFHSEQALAYGTKVVGGVTPGKGGQTHLD
LPVFNTMKEAVKETGADASVIYVPAPFVLDSIVEAVDSGVGLVVVITEGV
PTLDMLKAKRYLETNGNGTRLVGPNCPGVITPGECKIGIMPGHIHTPGRI
GIISRSGTLTYEAVAQTTNLGLGQSTCIGIGGDPIPGMNQIDALKLFQED
PDTDAIIMIGEIGGTAEEEAAEYIQSNVTKPVVGYIAGVTAPKGKRMGHA
GAIISGGKGTAEEKFAAFEKAGIAYTRSPAELGTTMLEVLKAKGLA

Gene Nucleotide Sequence:  Sequence Viewer
ATGAGCGTATTGATTAATAAAGACACCAAAGTATTGGTTCAAGGTTTTAC
CGGTAAAAACGGTACTTTCCACTCCGAACAAGCTCTGGCTTACGGCACTA
AAGTTGTCGGCGGCGTTACCCCAGGCAAAGGCGGTCAAACCCACCTAGAC
CTGCCTGTATTCAACACCATGAAAGAAGCCGTTAAAGAAACCGGCGCTGA
CGCATCCGTGATTTACGTTCCCGCTCCGTTTGTGTTGGATTCTATCGTTG
AAGCCGTTGATTCAGGCGTAGGCTTGGTCGTTGTGATTACCGAAGGCGTT
CCAACTCTGGACATGCTCAAAGCCAAACGTTACTTGGAAACCAACGGCAA
CGGTACCCGCTTGGTCGGCCCTAACTGCCCGGGCGTGATTACTCCGGGCG
AGTGCAAAATCGGCATTATGCCGGGCCACATCCACACTCCGGGCCGCATC
GGTATTATTTCCCGTTCCGGTACATTGACTTACGAAGCCGTGGCACAAAC
CACCAACCTGGGCTTGGGTCAGTCAACCTGTATCGGTATCGGCGGCGACC
CGATTCCTGGTATGAACCAAATCGACGCACTGAAACTCTTCCAAGAAGAC
CCAGATACCGATGCCATCATCATGATTGGTGAAATCGGTGGTACTGCGGA
AGAAGAAGCAGCCGAATACATCCAATCCAACGTAACCAAACCTGTTGTCG
GTTACATCGCCGGTGTTACCGCTCCTAAAGGCAAACGCATGGGCCACGCC
GGTGCGATTATCTCCGGCGGTAAAGGTACTGCCGAAGAAAAATTCGCCGC
GTTTGAAAAAGCCGGTATCGCCTACACCCGCAGCCCTGCCGAGTTGGGCA
CGACGATGCTGGAAGTGTTGAAAGCAAAAGGTTTGGCA


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