1T3W - JenaLib

Title :   CRYSTAL STRUCTURE OF THE E.COLI DNAG C-TERMINAL DOMAIN (RESIDUES 434 TO 581)

Authors :   A. J. Oakley, K. V. Loscha, P. M. Schaeffer, E. Liepinsh, M. C. J. Wilce, G N. E. Dixon

Date :   28 Apr 04 (Deposition) - 02 Nov 04 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)

Keywords :   Dnag, Dna-Directed Rna Polymerase, E. Coli, Dna Replication, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Oakley, K. V. Loscha, P. M. Schaeffer, E. Liepinsh, G. Pintacuda, M. C. J. Wilce, G. Otting, N. E. Dixon
Crystal And Solution Structures Of The Helicase-Binding Domain Of Escherichia Coli Primase
J. Biol. Chem. V. 280 11495 2005
PubMed-ID: 15649896 | Reference-DOI: 10.1074/JBC.M412645200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:134
 aligned with DNAG_ECOLI | P0ABS5 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:134
                                   456       466       476       486       496       506       516       526       536       546       556       566       576    
           DNAG_ECOLI   447 KRTTMRILIGLLVQNPELATLVPPLENLDENKLPGLGLFRELVNTCLSQPGLTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARERTHGLSNEERLELWTLNQELAK 580
               SCOP domains d1t3wa_ A: DNA primase DnaG, C-terminal domain                                                                                         SCOP domains
               CATH domains 1t3wA00 A:447-580 DNAb Helicase; Chain A                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3w A 447 KRTTmRILIGLLVQNPELATLVPPLENLDENKLPGLGLFRELVNTCLSQPGLTTGQLLEHYRGTNNAATLEKLSmWDDIADKNIAEQTFTDSLNHmFDSLLELRQEELIARERTHGLSNEERLELWTLNQELAK 580
                                |  456       466       476       486       496       506       516    |  526       536     | 546       556       566       576    
                                |                                                                   521-MSE              542-MSE                                  
                              451-MSE

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with DNAG_ECOLI | P0ABS5 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:135
                                   456       466       476       486       496       506       516       526       536       546       556       566       576     
           DNAG_ECOLI   447 KRTTMRILIGLLVQNPELATLVPPLENLDENKLPGLGLFRELVNTCLSQPGLTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARERTHGLSNEERLELWTLNQELAKK 581
               SCOP domains d1t3wb_ B: DNA primase DnaG, C-terminal domain                                                                                          SCOP domains
               CATH domains 1t3wB00 B:447-581 DNAb Helicase; Chain A                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3w B 447 KRTTmRILIGLLVQNPELATLVPPLENLDENKLPGLGLFRELVNTCLSQPGLTTGQLLEHYRGTNNAATLEKLSmWDDIADKNIAEQTFTDSLNHmFDSLLELRQEELIARERTHGLSNEERLELWTLNQELAKK 581
                                |  456       466       476       486       496       506       516    |  526       536     | 546       556       566       576     
                              451-MSE                                                               521-MSE              542-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DNAG_ECOLI | P0ABS5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003896	DNA primase activity	Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006269	DNA replication, synthesis of RNA primer	The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:1990077	primosome complex	Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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