1G71 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA PRIMASE

Authors :   M. A. Augustin, R. Huber, J. T. Kaiser

Date :   08 Nov 00 (Deposition) - 10 Jan 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Zinc-Knuckle, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Augustin, R. Huber, J. T. Kaiser
Crystal Structure Of A Dna-Dependent Rna Polymerase (Dna Primase).
Nat. Struct. Biol. V. 8 57 2001
PubMed-ID: 11135672 | Reference-DOI: 10.1038/83060
(for further references see the PDB file header)

Molecule 1 - DNA PRIMASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET 22 B (+)
	Expression System Strain	:	BL 21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	SO4	4	Ligand/Ion	SULFATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:106 , HIS A:108 , CYS A:114 , CYS A:117	BINDING SITE FOR RESIDUE ZN A 348
02	AC2	SOFTWARE	CYS B:106 , HIS B:108 , CYS B:114 , CYS B:117	BINDING SITE FOR RESIDUE ZN B 348
03	AC3	SOFTWARE	ARG A:313 , SER B:47	BINDING SITE FOR RESIDUE CL B 349
04	AC4	SOFTWARE	GLY B:86	BINDING SITE FOR RESIDUE CL B 350
05	AC5	SOFTWARE	GLY A:86	BINDING SITE FOR RESIDUE CL A 349
06	AC6	SOFTWARE	TYR A:202 , ARG B:229	BINDING SITE FOR RESIDUE CL A 351
07	AC7	SOFTWARE	LYS A:311 , ARG A:313	BINDING SITE FOR RESIDUE CL B 351
08	AC8	SOFTWARE	LYS A:99 , ARG A:148 , ARG A:292 , HIS A:298 , HOH A:378 , HOH A:452 , HOH A:456 , HOH A:514	BINDING SITE FOR RESIDUE SO4 A 352
09	AC9	SOFTWARE	ARG B:148 , ARG B:292 , HIS B:298 , HOH B:439	BINDING SITE FOR RESIDUE SO4 B 352
10	BC1	SOFTWARE	ARG A:148 , HOH A:541	BINDING SITE FOR RESIDUE SO4 A 353
11	BC2	SOFTWARE	ARG B:148	BINDING SITE FOR RESIDUE SO4 B 353

(no "SS Bond" information available for 1G71)

(no "Cis Peptide Bond" information available for 1G71)

(no "SAP(SNP)/Variant" information available for 1G71)

(no "PROSITE Motif" information available for 1G71)

(no "Exon" information available for 1G71)

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:344
 aligned with PRIS_PYRFU | Q9P9H1 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:344
                                    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    
           PRIS_PYRFU     1 MLMREVTKEERSEFYSKEWSAKKIPKFIVDTLESREFGFDHNGEGPSDRKNQYSDIRDLEDYIRATSPYAVYSSVAFYENPREMEGWRGAELVFDIDAKDLPLKRCNHEPGTVCPICLEDAKELAKDTLIILREELGFENIHVVYSGRGYHIRILDEWALQLDSKSRERILAFISASEIENVEEFRRFLLEKRGWFVLKHGYPRVFRLRLGYFILRVNVPHLLSIGIRRNIAKKILDHKEEIYEGFVRKAILASFPEGVGIESMAKLFALSTRFSKAYFDGRVTVDIKRILRLPSTLHSKVGLIATYVGTKEREVMKFNPFRHAVPKFRKKEVREAYKLWRESL 344
               SCOP domains d1g71a_ A: DNA primase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1g71A01 A:1-171,A:280-344 DNA primase, PRIM domain                                                                                                                         1g71A02 A:172-279 DNA primase S; domain 2                                                                   1g71A01 A:1-171,A:280-344 DNA primase, PRIM domain                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee.......eeee...hhhhhhhhhhhhh..eeeee.eeeeehhhheeeeee.eeeeee................hhhhhhhhhhhhhhhhhhhhhh.....eeeee...eeeeee.hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh...hhhhhhh...eee....ee....ee.eeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g71 A   1 MLMREVTKEERSEFYSKEWSAKKIPKFIVDTLESREFGFDHNGEGPSDRKNQYSDIRDLEDYIRATSPYAVYSSVAFYENPREMEGWRGAELVFDIDAKDLPLKRCNHEPGTVCPICLEDAKELAKDTLIILREELGFENIHVVYSGRGYHIRILDEWALQLDSKSRERILAFISASEIENVEEFRRFLLEKRGWFVLKHGYPRVFRLRLGYFILRVNVPHLLSIGIRRNIAKKILDHKEEIYEGFVRKAILASFPEGVGIESMAKLFALSTRFSKAYFDGRVTVDIKRILRLPSTLHSKVGLIATYVGTKEREVMKFNPFRHAVPKFRKKEVREAYKLWRESL 344
                                    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

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with PRIS_PYRFU | Q9P9H1 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:344
                                    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    
           PRIS_PYRFU     1 MLMREVTKEERSEFYSKEWSAKKIPKFIVDTLESREFGFDHNGEGPSDRKNQYSDIRDLEDYIRATSPYAVYSSVAFYENPREMEGWRGAELVFDIDAKDLPLKRCNHEPGTVCPICLEDAKELAKDTLIILREELGFENIHVVYSGRGYHIRILDEWALQLDSKSRERILAFISASEIENVEEFRRFLLEKRGWFVLKHGYPRVFRLRLGYFILRVNVPHLLSIGIRRNIAKKILDHKEEIYEGFVRKAILASFPEGVGIESMAKLFALSTRFSKAYFDGRVTVDIKRILRLPSTLHSKVGLIATYVGTKEREVMKFNPFRHAVPKFRKKEVREAYKLWRESL 344
               SCOP domains d1g71b_ B: DNA primase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1g71B01 B:1-171,B:280-344 DNA primase, PRIM domain                                                                                                                         1g71B02 B:172-279 DNA primase S; domain 2                                                                   1g71B01 B:1-171,B:280-344 DNA primase, PRIM domain                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee.......eeee...hhhhhhhhhhhhh..eeeee.eeeeehhhheeeeee.eeeeee................hhhhhhhhhhhhhhhhhhhhhh.....eeeee...eeeeee.hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh...hhhhhhh...eee....ee....ee.eeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g71 B   1 MLMREVTKEERSEFYSKEWSAKKIPKFIVDTLESREFGFDHNGEGPSDRKNQYSDIRDLEDYIRATSPYAVYSSVAFYENPREMEGWRGAELVFDIDAKDLPLKRCNHEPGTVCPICLEDAKELAKDTLIILREELGFENIHVVYSGRGYHIRILDEWALQLDSKSRERILAFISASEIENVEEFRRFLLEKRGWFVLKHGYPRVFRLRLGYFILRVNVPHLLSIGIRRNIAKKILDHKEEIYEGFVRKAILASFPEGVGIESMAKLFALSTRFSKAYFDGRVTVDIKRILRLPSTLHSKVGLIATYVGTKEREVMKFNPFRHAVPKFRKKEVREAYKLWRESL 344
                                    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

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Prim-pol domain (8)

Superfamily: Prim-pol domain (8)

Family: PriA-like (4)

Protein domain: DNA primase (3)

Pyrococcus furiosus [TaxId: 2261] (1)

1a	d1g71a_	A:
1b	d1g71b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: DNA primase, PRIM domain (3)

Homologous Superfamily: DNA primase, PRIM domain (3)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

1a	1g71A01	A:1-171,A:280-344
1b	1g71B01	B:1-171,B:280-344

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helicase, Ruva Protein; domain 3 (218)

Homologous Superfamily: DNA primase S; domain 2 (3)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

2a	1g71A02	A:172-279
2b	1g71B02	B:172-279

(no "Pfam Domain" information available for 1G71)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRIS_PYRFU | Q9P9H1)

molecular function
	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: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.
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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1dd9	STRUCTURE OF THE DNAG CATALYTIC CORE
1dde	STRUCTURE OF THE DNAG CATALYTIC CORE
1eqn	E.COLI PRIMASE CATALYTIC CORE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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