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2BPG

STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP

Functional Information from GO Data
ChainGOidnamespacecontents
A0001701biological_processin utero embryonic development
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005874cellular_componentmicrotubule
A0005876cellular_componentspindle microtubule
A0006259biological_processDNA metabolic process
A0006260biological_processDNA replication
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006287biological_processbase-excision repair, gap-filling
A0006290biological_processpyrimidine dimer repair
A0006297biological_processnucleotide-excision repair, DNA gap filling
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0006915biological_processapoptotic process
A0006954biological_processinflammatory response
A0006974biological_processDNA damage response
A0007435biological_processsalivary gland morphogenesis
A0008017molecular_functionmicrotubule binding
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0010332biological_processresponse to gamma radiation
A0016445biological_processsomatic diversification of immunoglobulins
A0016446biological_processsomatic hypermutation of immunoglobulin genes
A0016779molecular_functionnucleotidyltransferase activity
A0016829molecular_functionlyase activity
A0019899molecular_functionenzyme binding
A0032991cellular_componentprotein-containing complex
A0034061molecular_functionDNA polymerase activity
A0045471biological_processresponse to ethanol
A0046872molecular_functionmetal ion binding
A0048535biological_processlymph node development
A0048536biological_processspleen development
A0048872biological_processhomeostasis of number of cells
A0051402biological_processneuron apoptotic process
A0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
A0055093biological_processresponse to hyperoxia
A0071707biological_processimmunoglobulin heavy chain V-D-J recombination
A0071897biological_processDNA biosynthetic process
A0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
B0001701biological_processin utero embryonic development
B0003677molecular_functionDNA binding
B0003684molecular_functiondamaged DNA binding
B0003887molecular_functionDNA-directed DNA polymerase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005874cellular_componentmicrotubule
B0005876cellular_componentspindle microtubule
B0006259biological_processDNA metabolic process
B0006260biological_processDNA replication
B0006281biological_processDNA repair
B0006284biological_processbase-excision repair
B0006287biological_processbase-excision repair, gap-filling
B0006290biological_processpyrimidine dimer repair
B0006297biological_processnucleotide-excision repair, DNA gap filling
B0006303biological_processdouble-strand break repair via nonhomologous end joining
B0006915biological_processapoptotic process
B0006954biological_processinflammatory response
B0006974biological_processDNA damage response
B0007435biological_processsalivary gland morphogenesis
B0008017molecular_functionmicrotubule binding
B0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
B0010332biological_processresponse to gamma radiation
B0016445biological_processsomatic diversification of immunoglobulins
B0016446biological_processsomatic hypermutation of immunoglobulin genes
B0016779molecular_functionnucleotidyltransferase activity
B0016829molecular_functionlyase activity
B0019899molecular_functionenzyme binding
B0032991cellular_componentprotein-containing complex
B0034061molecular_functionDNA polymerase activity
B0045471biological_processresponse to ethanol
B0046872molecular_functionmetal ion binding
B0048535biological_processlymph node development
B0048536biological_processspleen development
B0048872biological_processhomeostasis of number of cells
B0051402biological_processneuron apoptotic process
B0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
B0055093biological_processresponse to hyperoxia
B0071707biological_processimmunoglobulin heavy chain V-D-J recombination
B0071897biological_processDNA biosynthetic process
B0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 500
ChainResidue
ATHR101
AVAL103
AILE106
PDC6

site_idAC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE DCT A 338
ChainResidue
AGLY189
AASP190
AASP192
ATYR271
APHE272
ATHR273
AASN279
PDC7
TDG4
TDG5
AARG149
AGLY179
ASER180
AARG183
ASER188

site_idAC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE DCT B 338
ChainResidue
BARG149
BSER180
BARG183
BSER188
BGLY189
BASP190
BASP192
BARG254
BTYR271
BASP276
CDG4
CDG5
DDC7

Functional Information from PROSITE/UniProt
site_idPS00522
Number of Residues20
DetailsDNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
ChainResidueDetails
AGLY179-PRO198

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000250|UniProtKB:P06746
ChainResidueDetails
AILE73
BILE73

site_idSWS_FT_FI2
Number of Residues26
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P06746
ChainResidueDetails
ALYS61
AASP190
AMET191
AVAL193
AILE257
BLYS61
BPRO63
BGLY66
BARG102
BTHR104
BGLY107
APRO63
BILE150
BPHE181
BGLY184
BASP190
BMET191
BVAL193
BILE257
AGLY66
AARG102
ATHR104
AGLY107
AILE150
APHE181
AGLY184

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
ChainResidueDetails
AILE73
BILE73

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000250|UniProtKB:P06746
ChainResidueDetails
ALYS84
AGLU153
BLYS84
BGLU153

site_idSWS_FT_FI5
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P06746
ChainResidueDetails
AALA42
ALEU62
ALEU82
BALA42
BLEU62
BLEU82

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1jms
ChainResidueDetails
AASP256

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1jms
ChainResidueDetails
BASP256

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PDB entries from 2024-07-24

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