2VOA - JenaLib

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Biological Unit 2 (Jmol Viewer)

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF AN AP ENDONUCLEASE FROM ARCHAEOGLOBUS FULGIDUS

Authors :   E. B. Kuettner, R. Schmiedel, T. Greiner-Stoffele, N. Strater

Date :   11 Feb 08 (Deposition) - 09 Dec 08 (Release) - 20 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Exoiii, Ap Endonuclease, Archaeoglobus Fulgidus, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Schmiedel, E. B. Kuettner, A. Keim, N. Strater, T. Greiner-Stoffele
Structure And Function Of The Abasic Site Specificity Pocket Of An Ap Endonuclease From Archaeoglobus Fulgidus.
Dna Repair V. 8 219 2009
PubMed-ID: 19015049 | Reference-DOI: 10.1016/J.DNAREP.2008.10.009
(for further references see the PDB file header)

Molecule 1 - EXODEOXYRIBONUCLEASE III
	Chains	:	A, B
	EC Number	:	4.2.99.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ORIGAMI B(DE3)-RIL
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Other Details	:	DSM4304
	Synonym	:	AF_EXO, XTHA

*Molecule 2 - 5'-D(GPCPGPGPTPAPGPCPCPGP)-3'*
	Chains	:	C
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPGPGPCPTPAPCPCPGPCP)-3'*
	Chains	:	D
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	OCS	-1	Mod. Amino Acid	CYSTEINESULFONIC ACID

(no "Site" information available for 2VOA)

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

Asymmetric Unit

No.	Residues
1	Glu A:84	-	Pro A:85
2	Glu B:84	-	Pro B:85

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

(no "PROSITE Motif" information available for 2VOA)

(no "Exon" information available for 2VOA)

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:257
 aligned with O29675_ARCFU | O29675 from UniProtKB/TrEMBL  Length:257

    Alignment length:257
                                    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       
         O29675_ARCFU     1 MLKIATFNVNSIRSRLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVCFHEDARRAYKKILELGFVDVLRKIHPNERIYTFYDYRVKGAIERGLGWRVDAILATPPLAERCVDCYADIKPRLAEKPSDHLPLVAVFDV 257
               SCOP domains d2voaa_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2voaA00 A:1-257  [code=3.60.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhh...eeeee..........hhhhhh...eeeee.......eeeee....eeee.............eeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhh.....eeeeeee............hhhh.......hhhhhhhhhhhhh.eeehhhhh...........................eeeeehhhhhh..eeeeehhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2voa A   1 MLKIATFNVNSIRSRLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVcFHEDARRAYKKILELGFVDVLRKIHPNERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDCYADIKPRLAEKPSDHLPLVAVFDV 257
                                    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       
                                                                                                                                                                                                167-OCS

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with O29675_ARCFU | O29675 from UniProtKB/TrEMBL  Length:257

    Alignment length:257
                                    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       
         O29675_ARCFU     1 MLKIATFNVNSIRSRLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVCFHEDARRAYKKILELGFVDVLRKIHPNERIYTFYDYRVKGAIERGLGWRVDAILATPPLAERCVDCYADIKPRLAEKPSDHLPLVAVFDV 257
               SCOP domains d2voab_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2voaB00 B:1-257  [code=3.60.10.10, no name defined]                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ----Exo_endo_phos-2voaB01 B:5-248                                                                                                                                                                                                                       --------- Pfam domains (1)
           Pfam domains (2) ----Exo_endo_phos-2voaB02 B:5-248                                                                                                                                                                                                                       --------- Pfam domains (2)
         Sec.struct. author .eeeeee........hhhhhhhhhhh...eeeee..........hhhhhh...eeeee.......eeeee....eeee.............eeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhh.....eeeeeee............hhhh.......hhhhhhhhhhhhh.eeehhhhh...........................eeeeehhhhhh..eeeee.............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2voa B   1 MLKIATFNVNSIRSRLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVcFHEDARRAYKKILELGFVDVLRKIHPNERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDCYADIKPRLAEKPSDHLPLVAVFDV 257
                                    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       
                                                                                                                                                                                                167-OCS

Chain C from PDB  Type:DNA  Length:10
                                          
                 2voa C   1 GCGGTAGCCG  10
                                    10

Chain D from PDB  Type:DNA  Length:10
                                          
                 2voa D   1 CGGCTACCGC  10
                                    10

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: automated matches (26)

Protein domain: automated matches (26)

Archaeoglobus fulgidus [TaxId: 2234] (1)

1a	d2voaa_	A:
1b	d2voab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Deoxyribonuclease I; Chain A (35)

Homologous Superfamily: [code=3.60.10.10, no name defined] (35)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1a	2voaA00	A:1-257
1b	2voaB00	B:1-257

Asymmetric Unit(hide GO term definitions)

Chain A,B (O29675_ARCFU | O29675)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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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	Sites
(no "Sites" information available for 2voa)

	Cis Peptide Bonds
		Glu A:84 - Pro A:85	[ RasMol ]
		Glu B:84 - Pro B:85	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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	2voa
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	O29675_ARCFU \| O29675
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