Rv3818 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Rieske (2Fe-2S) domain protein
- TUBERCULIST: Unknown protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: namH
  - function: N-glycosylation of peptidoglycan
  - reference: (Raymond 2005, PMID: 15522883)
Type: Essential
Start: 4282449
End: 4283999
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0051537 - 2 iron, 2 sulfur cluster binding (Uniprot)
- GO:0051536 - iron-sulfur cluster binding (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016042 - lipid catabolic process (FLUTE) (FLUTE Assigned!)
Reaction(s) (based on iSM810 metabolic model):
- NADPH[c] + UDPNAM[c] -> NADP[c] + UDPNGM[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): (none with >35% aa id)
Links to additional information on Rv3818:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.839 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VQVTSVGHAGFLIQTQAGSILCDPWVNPAYFASWFPFPDNSGLDWGALGECDYLYVSHLHKDHFDAENLRAHVNKDAVVLLPDFPVPDLRNELQKLGFHR
FFETTDSVKHRLRGPNGDLDVMIIALRAPADGPIGDSALVVADGETTAFNMNDARPVDLDVLASEFGHIDVHMLQYSGAIWYPMVYDMPARAKDAFGAQK
RQRQMDRARQYIAQVGATWVVPSAGPPCFLAPELRHLNDDGSDPANIFPDQMVFLDQMRAHGQDGGLLMIPGSTADFTGTTLNSLRHPLPAEQVEAIFTT
DKAAYIADYADRMAPVLAAQKAGWAAAAGEPLLQPLRTLFEPIMLQSNEICDGIGYPVELAIGPETIVLDFPKRAVREPIPDERFRYGFAIAPELVRTVL
RDNEPDWVNTIFLSTRFRAWRVGGYNEYLYTFFKCLTDERIAYADGWFAEAHDDSSSITLNGWEIQRRCPHLKADLSKFGVVEGNTLTCNLHGWQWRLDD
GRCLTARGHQLRSSRP

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 32 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000050; 4 non-insertions in a row out of 32 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 32 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.982550; 10 non-insertions in a row out of 32 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 32 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.65
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0238 (-)
- Rv3416 (whiB3)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3416 (whiB3)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0238 (-)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv3818 (-)

Property	Value	Creator	Evidence	PMID	Comment
Term	TBRXN:UAMRH UDP-MurNAc Hydroxylase - ISS	njamshidi	ISS	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818 authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. J. Bacteriol. 2005
Citation	Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka J. Biol. Chem. 2005	njamshidi	IPI	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
Term	TBRXN:UAMRH UDP-MurNAc Hydroxylase - IPI	njamshidi	IPI	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818 authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005
Citation	Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick J. Bacteriol. 2005	njamshidi	IPI	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
Term	TBRXN:UAMRH UDP-MurNAc Hydroxylase - IPI	njamshidi	IPI	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818 authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. J. Bacteriol. 2005
Citation	Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka J. Biol. Chem. 2005	njamshidi	ISS	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
Term	TBRXN:UAMRH UDP-MurNAc Hydroxylase - ISS	njamshidi	ISS	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818 authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005
Citation	Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick J. Bacteriol. 2005	njamshidi	ISS	15522883\|15805521	See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
Symbol	namH	mjackson	IMP		Peptidoglycan precursor synthesis
Name	N-acetylmuramic acid hydroxylase	mjackson	IMP		Peptidoglycan precursor synthesis
Citation	Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka J. Biol. Chem. 2005	jjmcfadden		15522883	Inferred from direct assay
Other	EC:	jjmcfadden			Inferred from direct assay authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005
Citation	Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka J. Biol. Chem. 2005	extern:JZUCKER		15522883	Inferred from direct assay
Term	EC:1.7.1.4 Nitrite reductase (NAD(P)H). - NR	extern:JZUCKER	NR		Inferred from direct assay authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005

Property

Value

Creator

Evidence

PMID

Comment

Term

TBRXN:UAMRH UDP-MurNAc Hydroxylase - ISS

njamshidi

ISS

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. J. Bacteriol. 2005

Citation

Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka J. Biol. Chem. 2005

njamshidi

IPI

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818

Term

TBRXN:UAMRH UDP-MurNAc Hydroxylase - IPI

njamshidi

IPI

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005

Citation

Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. authors,S. Mahapatra,T. Yagi,JT. Belisle,BJ. Espinosa,PJ. Hill,MR. McNeil,PJ. Brennan,DC. Crick J. Bacteriol. 2005

njamshidi

IPI

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818

Term

TBRXN:UAMRH UDP-MurNAc Hydroxylase - IPI

njamshidi

IPI

15522883|15805521

Citation

njamshidi

ISS

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818

Term

TBRXN:UAMRH UDP-MurNAc Hydroxylase - ISS

njamshidi

ISS

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818
authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005

Citation

njamshidi

ISS

15522883|15805521

See PMID: 15522883, 15805521. N glycolyation of N acetyl moiety. Bioechemically demonstrated in M smegmatis, must occur in some way in TB, BLAST search identified most likely candidate to be RV3818

Symbol

namH

mjackson

IMP

Peptidoglycan precursor synthesis

Name

N-acetylmuramic acid hydroxylase

mjackson

IMP

Peptidoglycan precursor synthesis

Citation

jjmcfadden

15522883

Inferred from direct assay

Other

EC:

jjmcfadden

Inferred from direct assay
authors,JB. Raymond,S. Mahapatra,DC. Crick,MS. Pavelka Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 2005

Citation

extern:JZUCKER

15522883

Inferred from direct assay

Term

EC:1.7.1.4 Nitrite reductase (NAD(P)H). - NR

extern:JZUCKER

Comments