3GXV - JenaLib

Title :   THREE-DIMENSIONAL STRUCTURE OF N-TERMINAL DOMAIN OF DNAB HELICASE FROM HELICOBACTER PYLORI AND ITS INTERACTIONS WITH PRIMASE

Authors :   T. Kashav, R. Nitharwal, A. A. Syed, A. Gabdoulkhakov, W. Saenger, K. S. Dhar, S. Gourinath

Date :   03 Apr 09 (Deposition) - 26 Jan 10 (Release) - 26 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Hexameric Helicase, Helicobacter Pylori, Primase, Replication, Atp-Binding, Autocatalytic Cleavage, Dna Replication, Dna-Binding Hydrolase, Nucleotide-Binding, Primosome, Dna-Binding, Helicase, Hydrolase, Hydrolase/Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kashav, R. Nitharwal, S. A. Abdulrehman, A. Gabdoulkhakov, W. Saenger, S. K. Dhar, S. Gourinath
Three-Dimensional Structure Of N-Terminal Domain Of Dnab Helicase And Helicase-Primase Interactions In Helicobacter Pylori
Plos One V. 4 E7515 2009
PubMed-ID: 19841750 | Reference-DOI: 10.1371/JOURNAL.PONE.0007515
(for further references see the PDB file header)

Compounds

Molecule 1 - REPLICATIVE DNA HELICASE
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 1-121
	Gene	:	HP_1362
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

Molecule 2 - REPLICATIVE DNA HELICASE
	Chains	:	C
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 101-122
	Gene	:	HP_1362
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

Molecule 3 - REPLICATIVE DNA HELICASE
	Chains	:	D
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 98-123
	Gene	:	HP_1362
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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:122
 aligned with DNAB_HELPY | O25916 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           DNAB_HELPY     1 MDHLKHLQQLQNIERIVLSGIVLANHKIEEVHSVLEPSDFYYPPNGLFFEIALKLHEEDCPIDENFIRQKMPKDKQIKEEDLVAIFAASPIDNIEAYVEEIKNASIKRKLFGLANTIREQAL 122
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxv A   1 MDHLKHLQQLQNIERIVLSGIVLANHKIEEVHSVLEPSDFYYPPNGLFFEIALKLHEEDCPIDENFIRQKMPKDKQIKEEDLVAIFAASPIDNIEAYVEEIKNASIKRKLFGLANTIREQAH 122
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with DNAB_HELPY | O25916 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
           DNAB_HELPY     1 MDHLKHLQQLQNIERIVLSGIVLANHKIEEVHSVLEPSDFYYPPNGLFFEIALKLHEEDCPIDENFIRQKMPKDKQIKEEDLVAIFAASPIDNIEAYVEEIKNASIKRKLFGLANTIREQALE 123
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxv B   1 MDHLKHLQQLQNIERIVLSGIVLANHKIEEVHSVLEPSDFYYPPNGLFFEIALKLHEEDCPIDENFIRQKMPKDKQIKEEDLVAIFAASPIDNIEAYVEEIKNASIKRKLFGLANTIREQAHH 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:22
 aligned with DNAB_HELPY | O25916 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:22
                                   110       120  
           DNAB_HELPY   101 IKNASIKRKLFGLANTIREQAL 122
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 3gxv C 101 IKNASIKRKLFGLANTIREQAL 122
                                   110       120

Chain D from PDB  Type:PROTEIN  Length:26
 aligned with DNAB_HELPY | O25916 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:26
                                   107       117      
           DNAB_HELPY    98 VEEIKNASIKRKLFGLANTIREQALE 123
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 3gxv D  98 VEEIKNASIKRKLFGLANTIREQALE 123
                                   107       117

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DNAB_HELPY | O25916)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003678	DNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	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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	3gxv
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