1V0G - JenaLib

Theoretical Model (Jmol Viewer)

Title :   THEORETICAL MODEL STRUCTURE OF DNAA A, DNA BINDING PROTEIN FROM RALSTONIA SOLANACEARUM

Authors :   S. Mahanta, C. Baruah, J. Deka, A. K. Buragohain

Date :   29 Mar 04 (Deposition) - 31 Mar 04 (Release) - 31 Mar 04 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Dna Binding Protein, Atp Binding, Dnaa Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mahanta, C. Baruah, J. Deka, A. K. Buragohain
Theoretical Structure Of Dnaa, A Dna Binding Protein Of Ralstonia Solanacearum
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
	Chains	:	A
	Organism Scientific	:	RALSTONIA SOLANACEARUM
	Strain	:	GMI1000
	Synonym	:	DNAA


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1V0G)

(no "Site" information available for 1V0G)

(no "SS Bond" information available for 1V0G)

(no "Cis Peptide Bond" information available for 1V0G)

(no "SAP(SNP)/Variant" information available for 1V0G)

Theoretical Model (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNAA	PS01008	DnaA protein signature.	DNAA_RALSO	480-499	1	A:480-499

(no "Exon" information available for 1V0G)

Theoretical Model

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:522
 aligned with DNAA_RALSO | Q8XTV4 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:522
                                    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       410       420       430       440       450       460       470       480       490       500       510       520  
           DNAA_RALSO     1 MQDFWHAASAQLESELTPQQFKTWIKPLTPLSFDEQACMLRIAAPNRFKLDWVKSQFSGRIQSLACDYWEMQVDVQFVLDPTAGQRQAAMQPALAPMPMQPLAAQTMQAQAVPREAPARPTMAPYRETPMATAAHAAADIDVPVMDAAEASTQSYRVPAPAAPAVMGGLSAPPAAPVDDTVHERSRLNPILTFDNLVTGKANQLARAAAVQVANNPGKSYNPLYLYGGVGLGKTHLIHAIGNFMLMENPRARIRYIHAEQYVSDVVKAYQRKAFDDFKRYYHSLDLLLIDDIQFFSGKNRTQEEFFYAFEALIANRAQVIITSDTYPKEITGIDDRLISRFDSGLTVAIEPPELEMRVAILMKKAQAENVTVPEEVAFFVAKHLRSNVRELEGALRKILAYSNFHGKEITIEVTREALKDLLTVQNRQISVENIQKTCADFYNIKVADMYSKKRPANIARPRQIAMYLAKELTQKSLPEIGELFGGRDHTTVLHAVRKIADERSKDAQLNHELHVLEQTLKG 522
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................hhhhhh...............................................................hhhhh.....................hhhhhh......................................................hhhhhhhhhhhhhhhh......hhhhh..........hhhhhhhhh..hhhhhhhhhhhhhhhh..............eee.........eeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhh...hhhhhhhhhh....................hhhhhhhhh......hhhhhhhhh....hhhhhhhh...........................................hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: A:480-499----------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v0g A   1 MQDFWHAASAQLESELTPQQFKTWIKPLTPLSFDEQACMLRIAAPNRFKLDWVKSQFSGRIQSLACDYWEMQVDVQFVLDPTAGQRQAAMQPALAPMPMQPLAAQTMQAQAVPREAPARPTMAPYRETPMATAAHAAADIDVPVMDAAEASTQSYRVPAPAAPAVMGGLSAPPAAPVDDTVHERSRLNPILTFDNLVTGKANQLARAAAVQVANNPGKSYNPLYLYGGVGLGKTHLIHAIGNFMLMENPRARIRYIHAEQYVSDVVKAYQRKAFDDFKRYYHSLDLLLIDDIQFFSGKNRTQEEFFYAFEALIANRAQVIITSDTYPKEITGIDDRLISRFDSGLTVAIEPPELEMRVAILMKKAQAENVTVPEEVAFFVAKHLRSNVRELEGALRKILAYSNFHGKEITIEVTREALKDLLTVQNRQISVENIQKTCADFYNIKVADMYSKKRPANIARPRQIAMYLAKELTQKSLPEIGELFGGRDHTTVLHAVRKIADERSKDAQLNHELHVLEQTLKG 522
                                    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       410       420       430       440       450       460       470       480       490       500       510       520

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 1V0G)

(no "CATH Domain" information available for 1V0G)

(no "Pfam Domain" information available for 1V0G)

Theoretical Model(hide GO term definitions)

Chain A (DNAA_RALSO | Q8XTV4)

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:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	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.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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:0006270	DNA replication initiation	The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Theoretical Model
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	Cis Peptide Bonds
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1j1v	CRYSTAL STRUCTURE OF DNAA DOMAIN IV COMPLEXED WITH DNAABOX DNA
1l8q	CRYSTAL STRUCTURE OF DNA REPLICATION INITIATION FACTOR

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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Exons (0, 0)

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