2OWQ - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE

Authors :   N. Schormann, D. Chattopadhyay

Date :   16 Feb 07 (Deposition) - 24 Jul 07 (Release) - 29 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Uracil-Dna Glycosylase Fold In The Core: 3 Layers (A/B/A), And Parallel Beta-Sheet Of 4 Strands In The Order 2134; Novel Features: Beta-Sheets At N- And C-Terminus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Schormann, A. Grigorian, A. Samal, R. Krishnan, L. Delucas, D. Chattopadhyay
Crystal Structure Of Vaccinia Virus Uracil-Dna Glycosylase Reveals Dimeric Assembly
Bmc Struct. Biol. V. 7 45 2007
PubMed-ID: 17605817 | Reference-DOI: 10.1186/1472-6807-7-45

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Chains	:	A, B
	EC Number	:	3.2.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)PLYSS ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	D4R, VACWR109
	Mutation	:	YES
	Organism Scientific	:	VACCINIA VIRUS WESTERN RESERVE
	Organism Taxid	:	696871
	Synonym	:	UDG

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	IMD	3	Ligand/Ion	IMIDAZOLE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	IMD	4	Ligand/Ion	IMIDAZOLE
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	IMD	2	Ligand/Ion	IMIDAZOLE
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:69 , TYR A:70 , PHE A:79 , ASN A:120 , IMD A:401	BINDING SITE FOR RESIDUE CL A 219
2	AC2	SOFTWARE	ILE A:112 , HOH A:433 , THR B:5 , VAL B:6 , HOH B:419 , HOH B:477	BINDING SITE FOR RESIDUE SO4 B 219
3	AC3	SOFTWARE	GLY A:66 , ASP A:68 , TYR A:70 , ASN A:120 , CL A:219	BINDING SITE FOR RESIDUE IMD A 401
4	AC4	SOFTWARE	HIS B:8 , ALA B:34	BINDING SITE FOR RESIDUE IMD B 402
5	AC5	SOFTWARE	HIS A:8 , ALA A:34	BINDING SITE FOR RESIDUE IMD A 403
6	AC6	SOFTWARE	GLY B:66 , ASP B:68 , PRO B:69 , TYR B:70 , PRO B:78 , PHE B:79 , ASN B:120 , HOH B:466 , HOH B:479	BINDING SITE FOR RESIDUE GOL B 301
7	AC7	SOFTWARE	PRO B:10 , THR B:12 , THR B:14 , ASP B:47 , PHE B:50	BINDING SITE FOR RESIDUE GOL B 302
8	AC8	SOFTWARE	LYS B:160 , TYR B:180 , HIS B:181	BINDING SITE FOR RESIDUE GOL B 303
9	AC9	SOFTWARE	LYS A:160 , THR A:161 , TYR A:180 , HIS A:181	BINDING SITE FOR RESIDUE GOL A 304

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

Asymmetric Unit

No.	Residues
1	Ala A:9	-	Pro A:10
2	Ser A:43	-	Pro A:44
3	Ala B:9	-	Pro B:10
4	Ser B:43	-	Pro B:44

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCA	61-70	2	A:61-70 B:61-70
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCW	61-70	2	A:61-70 B:61-70

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCA	61-70	2	A:61-70 -
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCW	61-70	2	A:61-70 -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCA	61-70	2	- B:61-70
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_VACCW	61-70	2	- B:61-70

(no "Exon" information available for 2OWQ)

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:216
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
            UNG_VACCA     - --MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh.eeeeee....ee......hhhhhhhhhhhhhhhhh....eeeee.............--.eeeee.......--hhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owq A  -1 SHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLE--VTTIVGYHPAARD--FEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168  |  | 178       | -|      198       208       218
                                                                                                                                                                                                      171  |         186  |                             
                                                                                                                                                                                                         174            189

Chain A from PDB  Type:PROTEIN  Length:216
 aligned with UNG_VACCW | P04303 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
            UNG_VACCW     - --MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDYSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh.eeeeee....ee......hhhhhhhhhhhhhhhhh....eeeee.............--.eeeee.......--hhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owq A  -1 SHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLE--VTTIVGYHPAARD--FEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168  |  | 178       | -|      198       208       218
                                                                                                                                                                                                      171  |         186  |                             
                                                                                                                                                                                                         174            189

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:227
                                     1                                                                                                                                                                                                                         
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
            UNG_VACCA     - ---------MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------UDG-2owqB01 B:54-203                                                                                                                                  --------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------UDG-2owqB02 B:54-203                                                                                                                                  --------------- Pfam domains (2)
         Sec.struct. author ..........eeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee..............-.eeeee.......--hhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owq B  -8 SGLVPRGSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLES-VTTIVGYHPAARD--FEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171| |    181    |  191       201       211       
                                                                                                                                                                                                              172 |         186  |                             
                                                                                                                                                                                                                174            189

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with UNG_VACCW | P04303 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:227
                                     1                                                                                                                                                                                                                         
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
            UNG_VACCW     - ---------MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDYSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------UDG-2owqB01 B:54-203                                                                                                                                  --------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------UDG-2owqB02 B:54-203                                                                                                                                  --------------- Pfam domains (2)
         Sec.struct. author ..........eeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhhh...eeeee..............-.eeeee.......--hhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owq B  -8 SGLVPRGSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLES-VTTIVGYHPAARD--FEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171| |    181    |  191       201       211       
                                                                                                                                                                                                              172 |         186  |                             
                                                                                                                                                                                                                174            189

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 2OWQ)

(no "CATH Domain" information available for 2OWQ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: UDG] (24)

Family: UDG (24)

Vaccinia virus (strain Ankara) (VACV) (2)

1a	UDG-2owqB01	B:54-203
1b	UDG-2owqB02	B:54-203

Asymmetric Unit(hide GO term definitions)

Chain A,B (UNG_VACCA | Q91UM2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	Catalysis of the hydrolysis of any N-glycosyl bond.
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Chain A,B (UNG_VACCW | P04303)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	Catalysis of the hydrolysis of any N-glycosyl bond.
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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	Cis Peptide Bonds
		Ala A:9 - Pro A:10	[ RasMol ]
		Ala B:9 - Pro B:10	[ RasMol ]
		Ser A:43 - Pro A:44	[ RasMol ]
		Ser B:43 - Pro B:44	[ RasMol ]

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	2owq
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	UNG_VACCW \| P04303
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	3.2.2.-
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UniProtKB/Swiss-Prot
	UNG_VACCA \| Q91UM2	:	3nt7 4dof 4dog 4irb 4lzb 4qc9 4qca 5jx3
	UNG_VACCW \| P04303	:	4qcb 5jx0 5jx3 5jx8

1akz	HUMAN URACIL-DNA GLYCOSYLASE
2eug	E. COLI URACIL-DNA GLYCOSYLASE
2owr	CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 19)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File