3C1Y - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF BACTERIAL DNA DAMAGE SENSOR PROTEIN WITH CO-PURIFIED AND CO-CRYSTALLIZED LIGAND

Authors :   G. Witte, S. Hartung, K. Buttner, K. P. Hopfner

Date :   24 Jan 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Dna Damage, Dna Repair, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Witte, S. Hartung, K. Buttner, K. P. Hopfner
Structural Biochemistry Of A Bacterial Checkpoint Protein Reveals Diadenylate Cyclase Activity Regulated By Dna Recombination Intermediates
Mol. Cell V. 30 167 2008
PubMed-ID: 18439896 | Reference-DOI: 10.1016/J.MOLCEL.2008.02.020
(for further references see the PDB file header)

Molecule 1 - DNA INTEGRITY SCANNING PROTEIN DISA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	2BA	1	Ligand/Ion	(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	2BA	4	Ligand/Ion	(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	2BA	1	Ligand/Ion	(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	2BA	-1	Ligand/Ion	(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:75 , GLY A:76 , HIS A:93 , LEU A:94 , THR A:107 , ARG A:108 , THR A:111 , ASP B:75 , GLY B:76 , HIS B:93 , LEU B:94 , THR B:107 , ARG B:108 , THR B:111	BINDING SITE FOR RESIDUE 2BA A 358

(no "SS Bond" information available for 3C1Y)

(no "Cis Peptide Bond" information available for 3C1Y)

(no "SAP(SNP)/Variant" information available for 3C1Y)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAC	PS51794	Diadenylate cyclase (DAC) domain profile.	DISA_THEMA	8-148	2	A:8-148 B:8-148

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAC	PS51794	Diadenylate cyclase (DAC) domain profile.	DISA_THEMA	8-148	8	A:8-148 B:8-148

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAC	PS51794	Diadenylate cyclase (DAC) domain profile.	DISA_THEMA	8-148	1	A:8-148 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAC	PS51794	Diadenylate cyclase (DAC) domain profile.	DISA_THEMA	8-148	1	- B:8-148

(no "Exon" information available for 3C1Y)

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:349
 aligned with DISA_THEMA | Q9WY43 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:349
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
           DISA_THEMA     7 VPQELIEKIKLISPGTELRKALDDIINANFGALIFLVDDPKKYEDVIQGGFWLDTDFSAEKLYELSKMDGAIVLSEDITKIYYANVHLVPDPTIPTGETGTRHRTAERLAKQTGKVVIAVSRRRNIISLYYKNYKYVVNQVDFLISKVTQAISTLEKYKDNFNKLLSELEVLELENRVTLADVVRTLAKGFELLRIVEEIRPYIVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSLKHRKT 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhh...eeeee..hhhhhh..ee..eeeeee.hhhhhhhhh....eeee.....eeeeeeeee...........hhhhhhhhhhhhhhh.eeeee......eeee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DAC  PDB: A:8-148 UniProt: 8-148                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c1y A   7 VPQELIEKIKLISPGTELRKALDDIINANFGALIFLVDDPKKYEDVIQGGFWLDTDFSAEKLYELSKMDGAIVLSEDITKIYYANVHLVPDPTIPTGETGTRHRTAERLAKQTGKVVIAVSRRRNIISLYYKNYKYVVNQVDFLISKVTQAISTLEKYKDNFNKLLSELEVLELENRVTLADVVRTLAKGFELLRIVEEIRPYIVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSLKHRKT 355
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

Chain B from PDB  Type:PROTEIN  Length:349
 aligned with DISA_THEMA | Q9WY43 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:349
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
           DISA_THEMA     7 VPQELIEKIKLISPGTELRKALDDIINANFGALIFLVDDPKKYEDVIQGGFWLDTDFSAEKLYELSKMDGAIVLSEDITKIYYANVHLVPDPTIPTGETGTRHRTAERLAKQTGKVVIAVSRRRNIISLYYKNYKYVVNQVDFLISKVTQAISTLEKYKDNFNKLLSELEVLELENRVTLADVVRTLAKGFELLRIVEEIRPYIVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSLKHRKT 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhh...eeeeee.hhhhhh..ee..eeeeee.hhhhhhhhh....eeeee....eeeeeeeee...........hhhhhhhhhhhhhhh.eeeee......eeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhh.......hhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DAC  PDB: B:8-148 UniProt: 8-148                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c1y B   7 VPQELIEKIKLISPGTELRKALDDIINANFGALIFLVDDPKKYEDVIQGGFWLDTDFSAEKLYELSKMDGAIVLSEDITKIYYANVHLVPDPTIPTGETGTRHRTAERLAKQTGKVVIAVSRRRNIISLYYKNYKYVVNQVDFLISKVTQAISTLEKYKDNFNKLLSELEVLELENRVTLADVVRTLAKGFELLRIVEEIRPYIVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSLKHRKT 355
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

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 3C1Y)

(no "CATH Domain" information available for 3C1Y)

(no "Pfam Domain" information available for 3C1Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DISA_THEMA | Q9WY43)

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: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: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:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0019932	second-messenger-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via a second messenger; a small molecule or ion that can be quickly generated or released from intracellular stores, and can diffuse within the cell. Second-messenger signaling includes production or release of the second messenger, and effectors downstream of the second messenger that further transmit the signal within the cell.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	DISA_THEMA \| Q9WY43	:	3c1z 3c21 3c23 4yvz 4yxj 4yxm

3c1z	STRUCTURE OF A BACTERIAL DNA DAMAGE SENSOR PROTEIN, APO-FORM
3c21	STRUCTURE OF A BACTERIAL DNA DAMAGE SENSOR PROTEIN WITH REACTION PRODUCT
3c23	STRUCTURE OF A BACTERIAL DNA DAMAGE SENSOR PROTEIN COMPLEXED WITH ATP ANALOG(CORDYCEPIN)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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Gene Ontology (9, 9)

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