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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF BRCT DOMAIN OF TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE

Authors :   T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   17 May 05 (Deposition) - 17 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Brct Domain, Dna Polymerase, Teminal Deoxynucleotidyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of Brct Domain Of Terminal Deoxynucleotidyltransferase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - DEOXYNUCLEOTIDYLTRANSFERASE, TERMINAL VARIANT
	Chains	:	A
	EC Number	:	2.7.7.31
	Engineered	:	YES
	Expression System Plasmid	:	P040621-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	BRCA1 C-TURMINUS (BRCT) DOMAIN
	Gene	:	DNTT, TDT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2COE)

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(no "Cis Peptide Bond" information available for 2COE)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_058200	R	112	G	TDT_HUMAN	Polymorphism	6584066	A	G	101	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TDT_HUMAN	27-124	1	A:16-113

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000371174	1b	ENSE00001826240	chr10:98064153-98064457	305	TDT_HUMAN	1-68	68	1	A:1-57 (gaps)	64
1.2	ENST00000371174	2	ENSE00000717360	chr10:98078109-98078283	175	TDT_HUMAN	68-126	59	1	A:57-115	59
1.3	ENST00000371174	3	ENSE00000717371	chr10:98079019-98079147	129	TDT_HUMAN	127-169	43	1	A:116-120	5
1.4	ENST00000371174	4	ENSE00000717393	chr10:98080375-98080545	171	TDT_HUMAN	170-226	57	0	-	-
1.5	ENST00000371174	5	ENSE00000717410	chr10:98082414-98082485	72	TDT_HUMAN	227-250	24	0	-	-
1.6	ENST00000371174	6	ENSE00000717425	chr10:98084023-98084146	124	TDT_HUMAN	251-292	42	0	-	-
1.7	ENST00000371174	7	ENSE00000717478	chr10:98087225-98087357	133	TDT_HUMAN	292-336	45	0	-	-
1.8	ENST00000371174	8	ENSE00000717489	chr10:98088482-98088587	106	TDT_HUMAN	336-371	36	0	-	-
1.9	ENST00000371174	9	ENSE00000717504	chr10:98092108-98092353	246	TDT_HUMAN	372-453	82	0	-	-
1.10a	ENST00000371174	10a	ENSE00000811044	chr10:98095648-98095731	84	TDT_HUMAN	454-481	28	0	-	-
1.11b	ENST00000371174	11b	ENSE00001856643	chr10:98097895-98098321	427	TDT_HUMAN	482-509	28	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:120
 aligned with TDT_HUMAN | P04053 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:138
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        
            TDT_HUMAN     5 RASHLSPRKKRPRQTGALMASSPQDIKFQDLVVFILEKKMGTTRRAFLMELARRKGFRVENELSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDVSWLIECIRAGKPVEMTGKHQLVVRRDYSDSTNPGPPKT 142
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......-------..................eeeee....hhhhhhhhhhhhhhh..ee.........eeee...hhhhhhhhhhhh........eeeehhhhhhhhhh.............-----------..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------G------------------------------ SAPs(SNPs)
                    PROSITE ----------------------BRCT  PDB: A:16-113 UniProt: 27-124                                                               ------------------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:1-57 (gaps) UniProt: 1-68 [INCOMPLETE]        ----------------------------------------------------------Exon 1.3         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.2  PDB: A:57-115 UniProt: 68-126                    ---------------- Transcript 1 (2)
                 2coe A   1 GSSGSS-------GTGALMASSPQDIKFQDLVVFILEKKMGTTRRALLMELARRKGFRVENELSDSVTHIVAENNSGSDVLEWLQAQKVQVSSQPELLDVSWLIECIGAGKPVEMTGKHQLS-----------GPSSG 120
                                 |   -   |    13        23        33        43        53        63        73        83        93       103       113 |       -   |    
                                 6       7                                                                                                         115         116

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(no "SCOP Domain" information available for 2COE)

(no "CATH Domain" information available for 2COE)

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NMR Structure(hide GO term definitions)

Chain A (TDT_HUMAN | P04053)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003912	DNA nucleotidylexotransferase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
	GO:0034061	DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006304	DNA modification	The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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