SGID Silkworm Genome Informatics Database
Gene
KWMTBOMO09629  Validated by peptides from experiments
Pre Gene Modal
BGIBMGA012855
Annotation
PREDICTED:_DNA_replication_ATP-dependent_helicase/nuclease_DNA2_[Amyelois_transitella]
Full name
Ubiquinone biosynthesis O-methyltransferase, mitochondrial       + More
DNA replication ATP-dependent helicase/nuclease DNA2      
Alternative Name
3-demethylubiquinol 3-O-methyltransferase
Polyprenyldihydroxybenzoate methyltransferase
DNA replication ATP-dependent helicase-like homolog
Location in the cell
Nuclear   Reliability : 3.119
 

Sequence

CDS
ATGAATAAAGAAACAGATACGAATAAAAAATTAAAGCAAATTAAAATAGAAAATAAAGATCCTTTAAAACAACTTGAACATTCTCCAATATTCAACAGCTTACCTGATATATCAAATTTACAATGTTTCACATTTGACAAAAAAGATTTTGAACAAGATGATGTAAGTGATGTTTTCAATGATGATTGGGAGCACGAAGAGGATGCAGCAGCCTTTGACAAGTTAAATCTGAATAAAATGCAGAGATGTGAGGTAATCAGTTTGAAAAATCATGAAAACAAAATGGAACTTTTTTTAAAGAGCGGTGAAATGACTGGCACTTGTTTTGTTGAAGGGATATGGAAATCAATACCTTTGAGTCCGGGCGATATAATCAGTGTGATTGCAGCTAAAAATGAAACGGGGCAACATTATTTAAACGACACAACTGGGCTGCTCGTTCTCCGTCCGGACCACTTGATATCGAGCACAAGTGTTGTGGCTGGAGTGTTTTGTAAGCGAAAAGCTGTACTCCAAGAGAGATGGAGAGGAATAGACTCTGCCAATACGGCGATGACAATTGGAATAATGGTACATGAGCTAGTACAAAAGGCTCTGACACAACAAATATCAGATATAACTCAGTTACGTTTAGAAGCTGATAGAATGATAAGGGAGTCCATACAGATGTTGTACGACGCAGGGATGACCGAGGAGGAGACCCGGACAAGCATGCAGTGCTACATACAGCCTCTCAATGATTTCATGAAGAGCTATGTCGTTTCCAAGGCCAGTCATGGAATTATGCAAAATAACAAAGAAAACTGGAACGGTCATATTGATAAGGTTTTGGATATAGAAGAAAATATATGCTGTCCACAATTAGGACTGAAAGGGAAGATCGATGCCACTTTGCAAGTTACCGTACCTGAAAAAAATGGTCTCCAGAAAGCCATAGTTCCTTTAGAGTTGAAAAGTGGAAAGGCATCTGTGTCGGCAGAACATCGCGGCCAGCTCGTAATGTATGGAATGATGCTGAGCTTACACAGAAACGAAGACCCCACTGTGGCTTTACAACGTGGACTGTTGCTTTATTTGAGAGACAAAGTAGACGTGAGGGAGGTTAACTGTGGATACCCAGAGAGGCGCGACTTGGTAATGCTGAGGAATCAGTTAGTTGAAAATCTCGCTTCAGATCCCAAAGATCCAGATCCAGAACAGTTAACTGATATTGAAGATGCCTCATTTTTACTTCAGCAAAAGCTACCAGAACCGATCAATCATGAGAGAGCATGCACTAAATGTCCGTACTTATCCATTTGTTCTGTCCATTTGTGGCATTCGGGAGGCCCATCAGTCTCTGAAAATCATCCGCTGTCAAAGTTACAAGGCCAAGCACTAGGACACTTATCCAAAGGTCACATAAAATATTTCTTTCATTGGACGGCTTTACTTAAGATGGAAGAGAAATTTCAAACGAATTCATCACCTTTACAAGCCTTGTGGACTGAGAGTGCTGAAAAAAGAGAAAAAAGAGGGACTTGCATTCCCAATCTGAAAATAAAGGCAGTGGAGCAATCAGGTGAAAAACATCTTCACGTATTTCGACGTTCAGGTGTTAGATTAAATAGAGAGAAAGGACCTCAAGAGGGGGAGTTCGCAATAGTCAGTATCGAGGGCAGACCGTGGGTAGCCGCGGGAGTTGTCAGCTCAGTTAGTAGCGATGAAGTGCAGATACATTTGGAAAGAGACTTGAGTAAACGTCTCTGCGAAGACACATTGTACCACATCGATTCGTATGAGTCTTATTCAACTATTGTACAAAATCTGTCCAACCTCGGCGTCTTGCTTGAATACAGTGAAAGGTCGGAGCGGCTTCGAACTTTGATAATAGACAAAACGAAACCTCAGTTTGAGGCGAAGCTACCACGCGAAGTCGGCCGGCTCGGCATCAAGCTCATGCGCTCACTGAACATCGAACAGCAGCGAGCTGTACTAAAAGCTCTTTCTGCCCAGGATTACGCACTCCTCCAAGGTCTCCCGGGAACTGGGAAAACTCAAACCATTTCCGTGCTGATACAAATGCTAGTTGGACTCAAACAAAGAGTACTAGTGACTGCTCACACGCACTCGGCGGTCGACACTCTGTTGAGTAGATTACCAGAGACTATGAAAGTGATGCGGTTGGGTTCGACGGCACGTGTTGATATAAATCTGCTACATCGCACCGAGAAACAATTAACAGCTTCTTGTCGCACCGTCGAAGAGCTAGCAAGACTGTACGATTCAATGGAAGTCATTGGTGTAACATGTTTGGGGTCCACGCACGCCATACTCTCTAGAACGACGTTCGACATGTGCATTGTTGATGAAGCTACCCAGGTATTACAATGCACGGTATTGAGACCACTGTTTGCTGCTAGAAGATTCTTGCTAGTTGGTGATCCCAAACAACTCCCGCCTATCGTGAAAAGTCGCGCCGCAAGGCGTCTCGGCATGGAAGAGAGTCTGTTCCACAGATTAATGGACGAAGAAGCAACTTGCACCTTGCATCTGCAGTATCGCATGAATCAAGCTATAACCGATGTAGCGAATCAAGTAGCTTATGACTCGCGTTTGAAATGTGCCAACGGACAAGTTGCTCTAGCTACACTCAGTATTGATATGCAGAAATTATCATCAAAAACGGAATGGTTAAAGAGAGCTTGCAGTCCAGAACCTGAAGACGCTGTATTGTTTTTGGACATGAAATCTACAAATGTGTTTGATTTTGAAAATGAAAGCCGCTCGTGTAGGAACAAAGCCGAAGCTTGCCTAGTTCTCGACTTGATGGAATGCTTCAAAGAGGGTGGCGTTTCATCTAAAAATATAGGTATAATAGCGCCATATCGCGAACAAGTGTCACTACTGCGCAGGGCCCTGGCGTCCTACTCTGTAGAAGTTAACACTGTTGATCAGTTCCAAGGCAGAGACAAGTCCATTTTAATATATTCGTGTACCAAATGGAATGTAAGCGAAGATCATAAAGTTAAGGAAGGAGAGATACTGAACGACGATCGGAGATTAGCTGTGAGCGTGACTCGAGCGAAGCACAAGTTCATTATAGTTGGTAATTCAAAAGCGTTGCATTGCTACGTCCCACTGCAACGGCTGATACGAGCAAGCGCTACTGTCAGTCTCAATGATGATATTGTTAAATGTTTGTATCATAAGTATAAAGAAATCATGATTTAG
Protein
MNKETDTNKKLKQIKIENKDPLKQLEHSPIFNSLPDISNLQCFTFDKKDFEQDDVSDVFNDDWEHEEDAAAFDKLNLNKMQRCEVISLKNHENKMELFLKSGEMTGTCFVEGIWKSIPLSPGDIISVIAAKNETGQHYLNDTTGLLVLRPDHLISSTSVVAGVFCKRKAVLQERWRGIDSANTAMTIGIMVHELVQKALTQQISDITQLRLEADRMIRESIQMLYDAGMTEEETRTSMQCYIQPLNDFMKSYVVSKASHGIMQNNKENWNGHIDKVLDIEENICCPQLGLKGKIDATLQVTVPEKNGLQKAIVPLELKSGKASVSAEHRGQLVMYGMMLSLHRNEDPTVALQRGLLLYLRDKVDVREVNCGYPERRDLVMLRNQLVENLASDPKDPDPEQLTDIEDASFLLQQKLPEPINHERACTKCPYLSICSVHLWHSGGPSVSENHPLSKLQGQALGHLSKGHIKYFFHWTALLKMEEKFQTNSSPLQALWTESAEKREKRGTCIPNLKIKAVEQSGEKHLHVFRRSGVRLNREKGPQEGEFAIVSIEGRPWVAAGVVSSVSSDEVQIHLERDLSKRLCEDTLYHIDSYESYSTIVQNLSNLGVLLEYSERSERLRTLIIDKTKPQFEAKLPREVGRLGIKLMRSLNIEQQRAVLKALSAQDYALLQGLPGTGKTQTISVLIQMLVGLKQRVLVTAHTHSAVDTLLSRLPETMKVMRLGSTARVDINLLHRTEKQLTASCRTVEELARLYDSMEVIGVTCLGSTHAILSRTTFDMCIVDEATQVLQCTVLRPLFAARRFLLVGDPKQLPPIVKSRAARRLGMEESLFHRLMDEEATCTLHLQYRMNQAITDVANQVAYDSRLKCANGQVALATLSIDMQKLSSKTEWLKRACSPEPEDAVLFLDMKSTNVFDFENESRSCRNKAEACLVLDLMECFKEGGVSSKNIGIIAPYREQVSLLRRALASYSVEVNTVDQFQGRDKSILIYSCTKWNVSEDHKVKEGEILNDDRRLAVSVTRAKHKFIIVGNSKALHCYVPLQRLIRASATVSLNDDIVKCLYHKYKEIMI

Summary

Description
O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway.
Key enzyme involved in DNA replication and DNA repair in nucleus and mitochondrion. Involved in Okazaki fragments processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. Also involved in 5'-end resection of DNA during double-strand break (DSB) repair: recruited by BLM and mediates the cleavage of 5'-ssDNA, while the 3'-ssDNA cleavage is prevented by the presence of RPA. Also involved in DNA replication checkpoint independently of Okazaki fragments processing. Possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5'-3' helicase and endonuclease activities. While the ATPase and endonuclease activities are well-defined and play a key role in Okazaki fragments processing and DSB repair, the 5'-3' DNA helicase activity is subject to debate. According to various reports, the helicase activity is weak and its function remains largely unclear. Helicase activity may promote the motion of DNA2 on the flap, helping the nuclease function (By similarity).
Catalytic Activity
3,4-dihydroxy-5-all-trans-polyprenylbenzoate + S-adenosyl-L-methionine = 3-methoxy,4-hydroxy-5-all-trans-polyprenylbenzoate + H(+) + S-adenosyl-L-homocysteine
a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + H(+) + S-adenosyl-L-homocysteine
ATP + H2O = ADP + H(+) + phosphate
Cofactor
[4Fe-4S] cluster
Subunit
Component of a multi-subunit COQ enzyme complex.
Interacts with BLM and WDHD1.
Similarity
Belongs to the class I-like SAM-binding methyltransferase superfamily. UbiG/COQ3 family.
Belongs to the ubiquitin-conjugating enzyme family.
Belongs to the DNA2/NAM7 helicase family.
Belongs to the mitochondrial carrier (TC 2.A.29) family.
Keywords
4Fe-4S   Acetylation   ATP-binding   Complete proteome   DNA damage   DNA repair   DNA replication   DNA-binding   Endonuclease   Helicase   Hydrolase   Iron   Iron-sulfur   Metal-binding   Mitochondrion   Multifunctional enzyme   Nuclease   Nucleotide-binding   Nucleus   Reference proteome  
Feature
chain  DNA replication ATP-dependent helicase/nuclease DNA2
EMBL
NWSH01002014    PCG69424.1    KQ459582    KPI98798.1    RSAL01000051    RVE50295.1    + More
AGBW02007651    OWR54970.1    PCG69423.1    KQ460208    KPJ16616.1    NEVH01027067    PNF13912.1    GEZM01007071    GEZM01007070    GEZM01007069    GEZM01007068    JAV95429.1    KQ982579    KYQ54573.1    GL762535    EFZ21261.1    KQ978881    KYN27838.1    AAZX01006541    LBMM01003817    KMQ93097.1    ADTU01018700    ADTU01018701    KQ976537    KYM81394.1    KK853205    KDR09858.1    GL435563    EFN73136.1    JRES01001015    KNC26103.1    KQ971321    EEZ99558.2    DS231818    EDS41370.1    GFDL01015201    JAV19844.1    GL887908    EGI69441.1    KQ434912    KZC11378.1    QOIP01000009    RLU18862.1    KK107119    EZA58765.1    CH933807    EDW12096.1    CP012528    ALC48772.1    KQ435826    KOX72024.1    NNAY01000651    OXU27176.1    JXUM01107199    KQ565122    KXJ71310.1    CH916368    EDW02974.1    JXUM01107195    KXJ71308.1    CM000162    EDX02897.1    ABLF02025366    GBXI01009199    JAD05093.1    CCAG010009805    JXJN01015446    GFXV01005271    MBW17076.1    AE014298    BT088860    AAN09623.1    ACS78060.1    CH954180    EDV46206.1    GDHF01018429    JAI33885.1    AAF46543.2    KZ288369    PBC26792.1    BT125972    ADX35951.1    CH964239    EDW81988.1    CH477188    EAT48794.1    BT006332    AAP20828.1    CH480830    EDW45669.1    CH940649    EDW63474.1    CM000366    EDX17541.1    KQ981693    KYN37622.1    ADMH02000009    ETN68108.1    CH902618    EDV38657.1    GAMC01005425    GAMC01005424    JAC01132.1    OUUW01000003    SPP78039.1    CVRI01000064    CRL05010.1    GGMS01014069    MBY83272.1    CH379065    EAL31468.1    AXCN02002217    GL450531    EFN80895.1    GGMR01006811    MBY19430.1    ATLV01023287    KE525342    KFB48819.1    AAAB01008026    EAA03204.4    GBHO01015567    JAG28037.1    GDIP01009317    JAM94398.1    APGK01045214    APGK01045215    APGK01045216    KB741032    ENN74756.1    GDIP01069629    JAM34086.1    GDIQ01075733    JAN19004.1    NEDP02076746    OWF34970.1    AJWK01012146    AJWK01012147    SPP78040.1    PNF13913.1    GBYB01007203    JAG76970.1    JH431646    HACA01016075    CDW33436.1    AXCM01003961    GFWV01013501    MAA38230.1    AABR07044935    GEDC01005166    JAS32132.1   
Pfam
PF13086   AAA_11        + More
PF08696   Dna2
PF13087   AAA_12
PF01930   Cas_Cas4
PF04117   Mpv17_PMP22
PF01245   Ribosomal_L19
PF00179   UQ_con
PF00153   Mito_carr
Interpro
IPR041679   DNA2/NAM7-like_AAA        + More
IPR027417   P-loop_NTPase       
IPR041677   DNA2/NAM7_AAA_11       
IPR014808   DNA_replication_fac_Dna2_N       
IPR026851   Dna2       
IPR011604   Exonuc_phg/RecB_C       
IPR022765   Dna2/Cas4_DUF83       
IPR014001   Helicase_ATP-bd       
IPR037151   AlkB-like_sf       
IPR003593   AAA+_ATPase       
IPR010233   UbiG_MeTrfase       
IPR029063   SAM-dependent_MTases       
IPR007248   Mpv17_PMP22       
IPR038657   L19_sf       
IPR001857   Ribosomal_L19       
IPR008991   Translation_prot_SH3-like_sf       
IPR023313   UBQ-conjugating_AS       
IPR000608   UBQ-conjugat_E2       
IPR016135   UBQ-conjugating_enzyme/RWD       
IPR002067   Mit_carrier       
IPR023395   Mt_carrier_dom_sf       
IPR018108   Mitochondrial_sb/sol_carrier       
IPR002167   Graves_DC       
SUPFAM
SSF52540   SSF52540        + More
SSF53335   SSF53335       
SSF50104   SSF50104       
SSF54495   SSF54495       
SSF103506   SSF103506       
PDB
5EAN     E-value=1.24353e-133,     Score=1225

Ontologies

Topology

Subcellular location
Mitochondrion inner membrane  
Nucleus  
Mitochondrion  
Length:
1070
Number of predicted TMHs:
0
Exp number of AAs in TMHs:
0.0366300000000002
Exp number, first 60 AAs:
0
Total prob of N-in:
0.00184
outside
1  -  1070
 
 

Population Genetic Test Statistics

Pi
287.183875
Theta
190.066637
Tajima's D
1.843364
CLR
0.134595
CSRT
0.855807209639518
Interpretation
Uncertain
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