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Title :   CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS PRIMASE (ZINC BINDING AND RNA POLYMERASE DOMAINS)

Authors :   J. E. Corn, P. J. Pease, G. L. Hura, J. M. Berger

Date :   26 Aug 05 (Deposition) - 15 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Zinc Ribbon, Toprim, Rna Polymerase, Dna Replication, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Corn, P. J. Pease, G. L. Hura, J. M. Berger
Crosstalk Between Primase Subunits Can Act To Regulate Primer Synthesis In Trans.
Mol. Cell V. 20 391 2005
PubMed-ID: 16285921 | Reference-DOI: 10.1016/J.MOLCEL.2005.09.004

Molecule 1 - DNA PRIMASE
	Chains	:	A
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET28B
	Expression System Strain	:	BL21(DE3) CODON+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZINC BINDING AND RNA POLYMERASE DOMAINS (RESIDUES 1-405)
	Gene	:	DNAG
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:35 , HIS A:38 , CYS A:56 , CYS A:59	BINDING SITE FOR RESIDUE ZN A 501

(no "SS Bond" information available for 2AU3)

(no "Cis Peptide Bond" information available for 2AU3)

(no "SAP(SNP)/Variant" information available for 2AU3)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	DNAG_AQUAE	243-324	1	A:243-324

(no "Exon" information available for 2AU3)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:403
 aligned with DNAG_AQUAE | O67465 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:403
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400   
           DNAG_AQUAE     1 MSSDIDELRREIDIVDVISEYLNLEKVGSNYRTNCPFHPDDTPSFYVSPSKQIFKCFGCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYVALDRVCDFYRESLLKNREASEYVKSRGIDPKVARKFDLGYAPSSEALVKVLKENDLLEAYLETKNLLSPTKGVYRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQNQANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLLSAGVEVYPVYLPEGYDPDEFIKEFGKEELRRLINSSGELFETLIKTARENLEEKTREFRYYLGFISDGVRRFALASEFHTKYKVPMEILLMKI 403
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2au3A01 A:1-97 DNA Primase; Chain A                                                              -------------------------------------------------------------------------------------------------------------------------------2au3A03 A:225-348  [code=3.40.1360.10, no name defined]                                                                     ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh..eee..eeee...........eeee....eeee.....eehhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhh...ee.......ee....eeeeeee.....eeeeeeee........eee.......hhhh.eehhhhhhhhhhhhh.eee..hhhhhhhhhhh....eeee.....hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: A:243-324 UniProt: 243-324                                           ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2au3 A   1 MSSDIDELRREIDIVDVISEYLNLEKVGSNYRTNCPFHPDDTPSFYVSPSKQIFKCFGCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYVALDRVCDFYRESLLKNREASEYVKSRGIDPKVARKFDLGYAPSSEALVKVLKENDLLEAYLETKNLLSPTKGVYRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQNQANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLLSAGVEVYPVYLPEGYDPDEFIKEFGKEELRRLINSSGELFETLIKTARENLEEKTREFRYYLGFISDGVRRFALASEFHTKYKVPMEILLMKI 403
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400

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 '\|'

(no "SCOP Domain" information available for 2AU3)

(no "Pfam Domain" information available for 2AU3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DNAG_AQUAE | O67465)

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: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: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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Description

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Ligands, Modified Residues, Ions (1, 1)

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