3NT7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL DNA GLYCOSYLASE R187V MUTANT

Authors :   D. Chattopadhyay

Date :   02 Jul 10 (Deposition) - 18 May 11 (Release) - 29 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Uracil-Dna Glycosylase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Druck Shudofsky, J. E. Silverman, D. Chattopadhyay, R. P. Ricciardi
Vaccinia Virus D4 Mutants Defective In Processive Dna Synthesis Retain Binding To A20 And Dna.
J. Virol. V. 84 12325 2010
PubMed-ID: 20861259 | Reference-DOI: 10.1128/JVI.01435-10

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Chains	:	C, A
	EC Number	:	3.2.2.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Gene	:	D4R, VACWR109
	Mutation	:	YES
	Organism Common	:	VACV
	Organism Scientific	:	VACCINIA VIRUS WESTERN RESERVE
	Organism Taxid	:	696871
	Synonym	:	UDG

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY C:159 , LYS C:160 , THR C:161 , TYR C:180 , HIS C:181	BINDING SITE FOR RESIDUE SO4 C 219
2	AC2	SOFTWARE	ARG A:98 , HOH A:238 , ARG C:98	BINDING SITE FOR RESIDUE SO4 C 220
3	AC3	SOFTWARE	ASN C:199	BINDING SITE FOR RESIDUE GOL C 221
4	AC4	SOFTWARE	GLY A:159 , LYS A:160 , TYR A:180 , HIS A:181	BINDING SITE FOR RESIDUE GOL A 219

(no "SS Bond" information available for 3NT7)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3NT7)

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 C:61-70

Biological Unit 1 (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	- C:61-70

Biological Unit 2 (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 -

Biological Unit 3 (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	4	A:61-70 C:61-70

(no "Exon" information available for 3NT7)

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:217
 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......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee...........---..eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nt7 A  -1 SHMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAK---PVTTIVGYHPAARDVQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168|   |  178       188       198       208       218
                                                                                                                                                                                                    169 173

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with UNG_VACCA | Q91UM2 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:219
                             1                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
            UNG_VACCA     - -MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------UDG-3nt7C01 C:54-203                                                                                                                                  --------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------UDG-3nt7C02 C:54-203                                                                                                                                  --------------- Pfam domains (2)
         Sec.struct. author .eeeee......eeeee.hhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhh......eeeee...................hhhhhhhhhhhhhhhh.....ee.hhhh..eeeee....ee......hhhhhhhhhhhhhhhhh....eeeee........------..eeeee.......hhhhhhhhhhhhhhhhhhh.....hhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nt7 C   0 HMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNI------PVTTIVGYHPAARDVQFEKDRSFEIINVLLELDNKAPINWAQGFIY 218
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159      |  -   |   179       189       199       209         
                                                                                                                                                                                                166    173

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 3NT7)

(no "CATH Domain" information available for 3NT7)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: UDG (24)

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

1a	UDG-3nt7C01	C:54-203
1b	UDG-3nt7C02	C:54-203

Asymmetric Unit(hide GO term definitions)

Chain A,C (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.

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

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	UNG_VACCA \| Q91UM2	:	2owq 4dof 4dog 4irb 4lzb 4qc9 4qca 5jx3

2owq	CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE
2owr	CRYSTAL STRUCTURE OF VACCINIA VIRUS URACIL-DNA GLYCOSYLASE

Description

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Sites (4, 4)

SS Bonds (0, 0)

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