RNHPH_MYCTU
ID RNHPH_MYCTU Reviewed; 364 AA.
AC P9WLH5; L0TBW1; P64955; Q10512;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 46.
DE RecName: Full=Bifunctional protein Rv2228c {ECO:0000303|PubMed:20363939};
DE Includes:
DE RecName: Full=Ribonuclease H {ECO:0000303|PubMed:20363939};
DE EC=3.1.26.4 {ECO:0000269|PubMed:20363939};
DE Includes:
DE RecName: Full=Adenosylcobalamin/alpha-ribazole phosphatase {ECO:0000305};
DE EC=3.1.3.73 {ECO:0000269|PubMed:20363939};
GN OrderedLocusNames=Rv2228c; ORFNames=MTCY427.09c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP CRYSTALLIZATION.
RC STRAIN=H37Rv;
RX PubMed=18678948; DOI=10.1107/s1744309108021118;
RA Watkins H.A., Baker E.N.;
RT "Cloning, expression, purification and preliminary crystallographic
RT analysis of the RNase HI domain of the Mycobacterium tuberculosis protein
RT Rv2228c as a maltose-binding protein fusion.";
RL Acta Crystallogr. F 64:746-749(2008).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 2-140, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, AND DOMAIN.
RC STRAIN=H37Rv;
RX PubMed=20363939; DOI=10.1128/jb.01615-09;
RA Watkins H.A., Baker E.N.;
RT "Structural and functional characterization of an RNase HI domain from the
RT bifunctional protein Rv2228c from Mycobacterium tuberculosis.";
RL J. Bacteriol. 192:2878-2886(2010).
CC -!- FUNCTION: Endonuclease that displays both RNase H activity with a
CC hybrid RNA/DNA substrate as well as double-stranded RNase activity. As
CC the only authenticated RNase HI in M.tuberculosis, probably plays an
CC important role in the physiology of this organism, being likely
CC involved in bacterial replication. {ECO:0000269|PubMed:20363939}.
CC -!- FUNCTION: Catalyzes the hydrolysis of the phospho group from alpha-
CC ribazole 5'-phosphate to form alpha-ribazole (PubMed:20363939). May
CC also catalyze the conversion of adenosylcobalamin 5'-phosphate to
CC adenosylcobalamin (vitamin B12) (By similarity). Has a possible role in
CC B12 recycling, but the primary role of the C-terminal domain of this
CC phosphatase enzyme could be phosphate generation to help bacterial
CC survival within the macrophage, which is a phosphate-deprived
CC environment (PubMed:20363939). {ECO:0000250|UniProtKB:P39701,
CC ECO:0000269|PubMed:20363939}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC Evidence={ECO:0000269|PubMed:20363939};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosylcob(III)alamin 5'-phosphate + H2O =
CC adenosylcob(III)alamin + phosphate; Xref=Rhea:RHEA:30367,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18408, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:60493; EC=3.1.3.73;
CC Evidence={ECO:0000250|UniProtKB:P39701};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-ribazole 5'-phosphate + H2O = alpha-ribazole +
CC phosphate; Xref=Rhea:RHEA:24456, ChEBI:CHEBI:10329,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:57918; EC=3.1.3.73;
CC Evidence={ECO:0000269|PubMed:20363939};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P0A7Y4, ECO:0000305|PubMed:20363939};
CC Note=Binds 2 divalent metal cations per subunit, which may be Mg(2+) or
CC Mn(2+), and which are essential for catalysis.
CC {ECO:0000305|PubMed:20363939};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=173 nM for a hybrid RNA/DNA substrate
CC {ECO:0000269|PubMed:20363939};
CC KM=172.6 nM for an RNA/RNA substrate {ECO:0000269|PubMed:20363939};
CC KM=5.5 mM for p-nitrophenol phosphate {ECO:0000269|PubMed:20363939};
CC KM=1.07 mM for alpha-ribazole 5'-phosphate
CC {ECO:0000269|PubMed:20363939};
CC Note=Vmax value for RNase H activity is identical to that for dsRNase
CC activity. {ECO:0000269|PubMed:20363939};
CC pH dependence:
CC Optimum pH is 4 for phosphatase activity using p-nitrophenol
CC phosphate as a substrate. {ECO:0000269|PubMed:20363939};
CC -!- PATHWAY: Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-
CC ribazole from 5,6-dimethylbenzimidazole: step 2/2.
CC -!- SUBUNIT: The N-terminal domain alone is monomeric in solution but
CC associates in the crystal to form a dimer.
CC {ECO:0000269|PubMed:20363939}.
CC -!- DOMAIN: Is composed of two domains, the N-terminal domain displays
CC RNase activity and the C-terminal domain has both acid phosphatase and
CC CobC activity, together with a role in enhancing the RNase H and
CC dsRNase activities of the N-terminal domain.
CC {ECO:0000269|PubMed:20363939}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the RNase H family.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the histidine
CC phosphatase superfamily. {ECO:0000305}.
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DR EMBL; AL123456; CCP45006.1; -; Genomic_DNA.
DR PIR; H70776; H70776.
DR RefSeq; NP_216744.1; NC_000962.3.
DR RefSeq; WP_003899226.1; NZ_NVQJ01000008.1.
DR PDB; 3HST; X-ray; 2.25 A; B/D=2-140.
DR PDBsum; 3HST; -.
DR AlphaFoldDB; P9WLH5; -.
DR SMR; P9WLH5; -.
DR STRING; 83332.Rv2228c; -.
DR PaxDb; P9WLH5; -.
DR DNASU; 888108; -.
DR GeneID; 45426206; -.
DR GeneID; 888108; -.
DR KEGG; mtu:Rv2228c; -.
DR TubercuList; Rv2228c; -.
DR eggNOG; COG0328; Bacteria.
DR eggNOG; COG0406; Bacteria.
DR OMA; GRWQIKH; -.
DR PhylomeDB; P9WLH5; -.
DR BRENDA; 3.1.26.4; 3445.
DR BRENDA; 3.1.3.73; 3445.
DR UniPathway; UPA00061; UER00517.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0043755; F:alpha-ribazole phosphatase activity; IDA:MTBBASE.
DR GO; GO:0071667; F:DNA/RNA hybrid binding; IDA:MTBBASE.
DR GO; GO:0032296; F:double-stranded RNA-specific ribonuclease activity; IDA:MTBBASE.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IDA:MTBBASE.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IDA:MTBBASE.
DR GO; GO:0006401; P:RNA catabolic process; IDA:MTBBASE.
DR CDD; cd07067; HP_PGM_like; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.40.50.1240; -; 1.
DR InterPro; IPR013078; His_Pase_superF_clade-1.
DR InterPro; IPR029033; His_PPase_superfam.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR014636; RNaseH/PGlycerate_mutase.
DR InterPro; IPR002156; RNaseH_domain.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00300; His_Phos_1; 1.
DR Pfam; PF13456; RVT_3; 1.
DR PIRSF; PIRSF036922; RNaseH_PGAM; 1.
DR SMART; SM00855; PGAM; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF53254; SSF53254; 1.
DR PROSITE; PS50879; RNASE_H_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Hydrolase; Magnesium; Metal-binding;
KW Multifunctional enzyme; Nuclease; Reference proteome.
FT CHAIN 1..364
FT /note="Bifunctional protein Rv2228c"
FT /id="PRO_0000103981"
FT DOMAIN 1..139
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT ACT_SITE 172
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P62707"
FT ACT_SITE 246
FT /note="Proton donor/acceptor; for phosphatase activity"
FT /evidence="ECO:0000250|UniProtKB:P62707"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7Y4,
FT ECO:0000305|PubMed:20363939"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P0A7Y4,
FT ECO:0000305|PubMed:20363939"
FT BINDING 49
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7Y4,
FT ECO:0000305|PubMed:20363939"
FT BINDING 73
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7Y4,
FT ECO:0000305|PubMed:20363939"
FT BINDING 123
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P0A7Y4,
FT ECO:0000305|PubMed:20363939"
FT STRAND 2..26
FT /evidence="ECO:0007829|PDB:3HST"
FT STRAND 31..43
FT /evidence="ECO:0007829|PDB:3HST"
FT HELIX 45..63
FT /evidence="ECO:0007829|PDB:3HST"
FT STRAND 66..73
FT /evidence="ECO:0007829|PDB:3HST"
FT HELIX 75..81
FT /evidence="ECO:0007829|PDB:3HST"
FT HELIX 90..103
FT /evidence="ECO:0007829|PDB:3HST"
FT STRAND 106..113
FT /evidence="ECO:0007829|PDB:3HST"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:3HST"
FT HELIX 120..135
FT /evidence="ECO:0007829|PDB:3HST"
SQ SEQUENCE 364 AA; 39145 MW; A78E00C9E7D42F9E CRC64;
MKVVIEADGG SRGNPGPAGY GAVVWTADHS TVLAESKQAI GRATNNVAEY RGLIAGLDDA
VKLGATEAAV LMDSKLVVEQ MSGRWKVKHP DLLKLYVQAQ ALASQFRRIN YEWVPRARNT
YADRLANDAM DAAAQSAAAD ADPAKIVATE SPTSPGWTGA RGTPTRLLLL RHGQTELSEQ
RRYSGRGNPG LNEVGWRQVG AAAGYLARRG GIAAVVSSPL QRAYDTAVTA ARALALDVVV
DDDLVETDFG AWEGLTFAEA AERDPELHRR WLQDTSITPP GGESFDDVLR RVRRGRDRII
VGYEGATVLV VSHVTPIKML LRLALDAGSG VLYRLHLDLA SLSIAEFYAD GASSVRLVNQ
TGYL
