XPB_MYCTU
ID XPB_MYCTU Reviewed; 549 AA.
AC O53873; F2GIZ2; I6WZM2;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 03-AUG-2022, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DNA helicase XPB {ECO:0000303|PubMed:19199647};
DE EC=3.6.4.12 {ECO:0000269|PubMed:19199647, ECO:0000269|PubMed:22615856};
GN Name=XPB {ECO:0000303|PubMed:19199647};
GN Synonyms=ercc3 {ECO:0000312|EMBL:CCP43609.1};
GN OrderedLocusNames=Rv0861c {ECO:0000312|EMBL:CCP43609.1};
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1] {ECO:0000312|EMBL:CCP43609.1}
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., Harris D.,
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., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton J.,
RA Squares R., Squares S., 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 PROTEIN SEQUENCE OF 2-27, AND SEQUENCE REVISION TO N-TERMINUS.
RC STRAIN=H37Rv;
RX PubMed=34915127; DOI=10.1016/j.ygeno.2021.12.001;
RA Shi J., Meng S., Wan L., Zhang Z., Jiang S., Zhu H., Dai E., Chang L.,
RA Gao H., Wan K., Zhang L., Zhao X., Liu H., Lyu Z., Zhang Y., Xu P.;
RT "Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct
RT annotated encoding genes.";
RL Genomics 114:292-304(2022).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF LYS-209 AND GLU-299.
RC STRAIN=H37Rv;
RX PubMed=19199647; DOI=10.1021/bi8022416;
RA Biswas T., Pero J.M., Joseph C.G., Tsodikov O.V.;
RT "DNA-dependent ATPase activity of bacterial XPB helicases.";
RL Biochemistry 48:2839-2848(2009).
RN [4] {ECO:0007744|PubMed:21969609}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.M111.011445;
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 [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND DNA-BINDING.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=22615856; DOI=10.1371/journal.pone.0036960;
RA Balasingham S.V., Zegeye E.D., Homberset H., Rossi M.L., Laerdahl J.K.,
RA Bohr V.A., Toenjum T.;
RT "Enzymatic activities and DNA substrate specificity of Mycobacterium
RT tuberculosis DNA helicase XPB.";
RL PLoS ONE 7:e36960-e36960(2012).
CC -!- FUNCTION: ATP-dependent 3'-5' DNA helicase, unwinds 3'-overhangs,
CC 3'- flaps, and splayed-arm DNA substrates but not 5'-overhangs, 5'-flap
CC substrates, 3-way junctions or Holliday junctions. Not highly efficient
CC in vitro (PubMed:19199647, PubMed:22615856). Requires ATP hydrolysis
CC for helicase activity; the ATPase activity is DNA-dependent and
CC requires a minimum of 4 single-stranded nucleotides (nt) with 6-10 nt
CC providing all necessary interactions for full processive unwinding. The
CC ATPase prefers ATP over CTP or GTP, is almost inactive with TTP
CC (PubMed:19199647). DNA helicase activity requires ATP or dATP and only
CC acts when the 3'-overhang is >20 nt. Capable of unwinding a DNA:RNA
CC hybrid if the 3'-overhang is DNA. Also catalyzes ATP-independent
CC annealing of complementary DNA strands; annealing requires Mg(2+)
CC (PubMed:22615856). {ECO:0000269|PubMed:19199647,
CC ECO:0000269|PubMed:22615856}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000269|PubMed:19199647, ECO:0000269|PubMed:22615856};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:19199647, ECO:0000269|PubMed:22615856};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19199647, ECO:0000269|PubMed:22615856};
CC Note=ATPase activity has a small preference for Mn(2+) over Mg(2+),
CC Ca(2+) supports ATPase activity less well. Co(2+) and Zn(2+) are
CC inactive (PubMed:19199647). Another study shows equal activity with
CC Mg(2+) and Mn(2+), none with Ca(2+) (PubMed:22615856).
CC {ECO:0000269|PubMed:19199647, ECO:0000269|PubMed:22615856};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=50 nM for 21-mer ssDNA substrate {ECO:0000269|PubMed:19199647};
CC KM=22 uM for 10-mer ssDNA substrate {ECO:0000269|PubMed:19199647};
CC Note=kcat is 10 sec(-1) on a ssDNA 21-mer and about 50 sec(-1) on
CC ssDNA 5kb template. {ECO:0000269|PubMed:19199647};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:19199647}.
CC -!- DOMAIN: Removal of the N-terminus decreases solubility and/or
CC structural integrity of the protein. {ECO:0000269|PubMed:19199647}.
CC -!- SIMILARITY: Belongs to the helicase family. RAD25/XPB subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CCP43609.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000269|PubMed:34915127};
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DR EMBL; AL123456; CCP43609.1; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_215376.3; NC_000962.3.
DR RefSeq; WP_003404428.1; NC_000962.3.
DR SMR; O53873; -.
DR STRING; 83332.Rv0861c; -.
DR PaxDb; O53873; -.
DR GeneID; 885425; -.
DR KEGG; mtu:Rv0861c; -.
DR PATRIC; fig|83332.111.peg.953; -.
DR TubercuList; Rv0861c; -.
DR eggNOG; COG1061; Bacteria.
DR OMA; LKLGWPA; -.
DR PhylomeDB; O53873; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR032438; ERCC3_RAD25_C.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR032830; XPB/Ssl2_N.
DR Pfam; PF16203; ERCC3_RAD25_C; 1.
DR Pfam; PF13625; Helicase_C_3; 1.
DR Pfam; PF04851; ResIII; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Direct protein sequencing; DNA-binding; Helicase; Hydrolase;
KW Magnesium; Manganese; Nucleotide-binding; Reference proteome.
FT CHAIN 1..549
FT /note="DNA helicase XPB"
FT /id="PRO_0000455759"
FT DOMAIN 190..344
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 399..545
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..130
FT /note="Required for protein stability or solubility"
FT /evidence="ECO:0000269|PubMed:19199647"
FT MOTIF 298..301
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 203..210
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 209
FT /note="K->E,R: Loss of ATPase activity."
FT /evidence="ECO:0000269|PubMed:19199647"
FT MUTAGEN 299
FT /note="E->A: Loss of ATPase activity."
FT /evidence="ECO:0000269|PubMed:19199647"
SQ SEQUENCE 549 AA; 60500 MW; EA22CE3690D598A8 CRC64;
MTDGPLIVQS DKTVLLEVDH ELAGAARAAI APFAELERAP EHVHTYRITP LALWNARAAG
HDAEQVVDAL VSYSRYAVPQ PLLVDIVDTM ARYGRLQLVK NPAHGLTLVS LDRAVLEEVL
RNKKIAPMLG ARIDDDTVVV HPSERGRVKQ LLLKIGWPAE DLAGYVDGEA HPISLHQEGW
QLRDYQRLAA DSFWAGGSGV VVLPCGAGKT LVGAAAMAKA GATTLILVTN IVAARQWKRE
LVARTSLTEN EIGEFSGERK EIRPVTISTY QMITRRTKGE YRHLELFDSR DWGLIIYDEV
HLLPAPVFRM TADLQSKRRL GLTATLIRED GREGDVFSLI GPKRYDAPWK DIEAQGWIAP
AECVEVRVTM TDSERMMYAT AEPEERYRIC STVHTKIAVV KSILAKHPDE QTLVIGAYLD
QLDELGAELG APVIQGSTRT SEREALFDAF RRGEVATLVV SKVANFSIDL PEAAVAVQVS
GTFGSRQEEA QRLGRILRPK ADGGGAIFYS VVARDSLDAE YAAHRQRFLA EQGYGYIIRD
ADDLLGPAI
