- PDB-1bpb: CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMM... -
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基本情報
登録情報
データベース: PDB / ID: 1bpb
タイトル
CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM
要素
DNA POLYMERASE BETA
キーワード
NUCLEOTIDYLTRANSFERASE
機能・相同性
機能・相同性情報
Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / microtubule / DNA replication / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
DNA POLYMERASE BETA POSSESSES A PROTEOLYTICALLY SENSITIVE REGION IN ITS AMINO ACID SEQUENCE ...DNA POLYMERASE BETA POSSESSES A PROTEOLYTICALLY SENSITIVE REGION IN ITS AMINO ACID SEQUENCE (RESIDUES 80 - 90), AND THE PRECISE CLEAVAGE SITE VARIES DEPENDING ON THE PROTEASE OR THE CHEMICAL REAGENT USED IN THE CLEAVAGE REACTION (SEE A. KUMAR ET AL., J. BIOL. CHEM. 265, 2124 (1990)). THE AUTHORS SUSPECT THAT A BACTERIAL PROTEASE OF UNKNOWN ORIGIN UNEXPECTEDLY CLEAVED THEIR INTACT ENZYME DURING THE CRYSTALLIZATION PROCESS, RESULTING IN CRYSTALS OF THE PROTEIN STRUCTURE REPORTED IN THIS ENTRY - THE 31-KD COOH-TERMINAL DOMAIN (RESIDUES 88 - 335) OF DNA POLYMERASE BETA. BECAUSE THE AUTHORS HAVE NOT DONE AN N-TERMINAL ANALYSIS ON THE PROTEIN IN THEIR CRYSTALS, THEIR CHOICE OF THE CLEAVAGE SITE (BETWEEN RESIDUES 87 AND 88) IS RATHER ARBITRARY, AND IN FACT, THERE MAY EVEN BE VARIABLE N-TERMINAL RESIDUES WITHIN ANY GIVEN CRYSTAL OF THIS CLEAVED PROTEIN. PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN AND THE FIRST 8 KD DOMAIN IS NOT PRESENT IN THIS STRUCTURE. PDB ADVISORY NOTICE: WATER MOLECULES 441, 468, AND 477 ARE VERY CLOSE TO SPECIAL POSITIONS.
配列の詳細
SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DPOB_RAT SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 227 LEU 228 THE PAPER BY KUMAR, ET AL., J.BIOL.CHEM., 265, 2124, (1990) REPORTS A CORRECTION TO THE SEQUENCE GIVEN IN SWISS-PROT (SEE REFERENCE 3 ABOVE).