TB Genome Annotation Portal

Rv0753c (mmsA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: methylmalonate-semialdehyde dehydrogenase (acylating)
  • REFSEQ: methylmalonate-semialdehyde dehydrogenase
  • PATRIC: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
  • TUBERCULIST: Probable methylmalonate-semialdehyde dehydrogenase MmsA (methylmalonic acid semialdehyde dehydrogenase) (MMSDH)
  • NCBI: Probable methylmalonate-semialdehyde dehydrogenase MmsA (methylmalonic acid semialdehyde dehydrogenase) (MMSDH)
  • updated information (H37Rv4):
    • gene name: mmsA
    • function:
    • reference:
• Type: Not Target
• Start: 844421
• End: 845953
• Operon:


• Trans-membrane region:
  
• Role: I.A.2 - Amino acids and amines
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0004491 - methylmalonate-semialdehyde dehydrogenase (acylating) activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • NAD[c] + COA[c] + METHYMALONATE[c] -> NADH[c] + CO2[c] + PROPIONYLCOA[c]
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  4IYM	67%	Sinorhizobium meliloti	Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934
  4E4G	67%	Sinorhizobium meliloti	Crystal structure of putative Methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021
  5TJR	55%	Pseudomonas sp. AAC	X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC
  4ZZ7	53%	Oceanimonas doudoroffii	Crystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas doudoroffii
  1T90	41%	Bacillus subtilis	Crystal structure of methylmalonate semialdehyde dehydrogenase from Bacillus subtilis
  4PZ2	37%	Zea mays	Structure of Zm ALDH2-6 (RF2F) in complex with NAD
  6WSB	35%	Burkholderia pseudomallei (strain 1710b)	Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei bound to cofactor NAD
  6WSA	35%	Burkholderia pseudomallei (strain 1710b)	Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei without cofactor
  4LIH	35%	Burkholderia cenocepacia	The crystal structure of Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase from Burkholderia cenocepacia J2315
  3R31	35%	Agrobacterium tumefaciens	Crystal structure of betaine aldehyde dehydrogenase from Agrobacterium tumefaciens

• Links to additional information on mmsA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.16 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTTQISHFIDGQRTAGQSTRSADVFDPNTGQIQAKVPMAGKSDIDAAVASAVEAQKGWAAWNPQRRARVLMRFIELVNDTIDELAELLSREHGKTLADAR
GDVQRGIEVIEFCLGIPHLLKGEYTEGAGPGIDVYSLRQPLGVVAGITPFNFPAMIPLWKAGPALACGNAFVLKPSERDPSVPVRLAELFIEAGLPAGVF
QVVHGDKEAVDAILHHPDIKAVGFVGSSDIAQYIYAGAAATGKRAQCFGGAKNHMIVMPDADLDQAVDALIGAGYGSAGERCMAISVAVPVGDQTAERLR
ARLIERINNLRVGHSLDPKADYGPLVTGAALARVRDYIGQGVAAGAELVVDGRDRASDDLTFGLPEGDANLEGGFFIGPTLFDHVAAHMSIYTDEIFGPV
LCMVRARDYEEALRLPSEHEYGNGVAIFTRDGDAARDFVSRVQVGMVGVNVPIPVPVAYHTFGGWKRSGFGDLNQHGPAAIQFYTKVKTVTSRWPSGIKD
GAEFVIPTMS

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	2.36 (0.49)	1.35 (0.54)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link