2UUG - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH H187D MUTANT UDG AND WILD-TYPE UGI

Authors :   C. D. Putnam, A. S. Arvai, C. D. Mol, J. A. Tainer

Date :   31 Oct 98 (Deposition) - 25 Mar 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Dna Base Excision Repair, Protein Mimicry Of Dna, Protein Inhibitor, Replication, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Putnam, M. J. Shroyer, A. J. Lundquist, C. D. Mol, A. S. Arvai, D. W. Mosbaugh, J. A. Tainer
Protein Mimicry Of Dna From Crystal Structures Of The Uracil-Dna Glycosylase Inhibitor Protein And Its Complex With Escherichia Coli Uracil-Dna Glycosylase
J. Mol. Biol. V. 287 331 1999
PubMed-ID: 10080896 | Reference-DOI: 10.1006/JMBI.1999.2605

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B
	EC Number	:	3.2.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	TAC
	Expression System Plasmid	:	PSB1051
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Expression System Vector	:	PKK223-3
	Expression System Vector Type	:	PLASMID
	Gene	:	UNG
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	UDG

Molecule 2 - URACIL-DNA GLYCOSYLASE INHIBITOR
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	TAC
	Expression System Plasmid	:	PZWTAC1
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Expression System Vector	:	PKK223-3
	Expression System Vector Type	:	PLASMID
	Gene	:	UGI
	Organism Scientific	:	BACILLUS PHAGE PBS2
	Organism Taxid	:	10684
	Synonym	:	UGI

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2UUG)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	GB1	AUTHOR	ASP A:64	GENERAL BASE TO ACTIVATE NUCLEOPHILIC WATER
2	GB2	AUTHOR	ASP B:64	GENERAL BASE TO ACTIVATE NUCLEOPHILIC WATER
3	UR1	AUTHOR	GLN A:63 , TYR A:66 , PHE A:77 , ASN A:123	URACIL BINDING RESIDUES BY HOMOLOGY
4	UR2	AUTHOR	GLN B:63 , TYR B:66 , PHE B:77 , ASN B:123	URACIL BINDING RESIDUES BY HOMOLOGY

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

Asymmetric Unit

No.	Residues
1	Tyr A:38	-	Pro A:39
2	Tyr B:38	-	Pro B:39
3	Ala C:62	-	Pro C:63
4	Ala D:62	-	Pro D:63

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

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_ECOLI	57-66	2	A:57-66 B:57-66

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_ECOLI	57-66	1	A:57-66 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_ECOLI	57-66	1	- B:57-66

(no "Exon" information available for 2UUG)

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:223
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224   
            UNG_ECOLI     5 LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAE 227
               SCOP domains d2uuga_ A: Uracil-DNA glycosylase                                                                                                                                                                                               SCOP domains
               CATH domains 2uugA00 A:5-227 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.hhhh..hhhhhhhhhhhhhhh........hhh..hhhhh.......eeeee........................hhhhhhhhhhhhh............hhhhhh.eeeee.................hhhhhhhhhhhhhhh....eeeee.hhhhhhh........eeeee....hhhhhh......hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------U_DNA_GLYC----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uug A   5 LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPDPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAE 227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with UNG_ECOLI | P12295 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:222
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224  
            UNG_ECOLI     5 LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPA 226
               SCOP domains d2uugb_ B: Uracil-DNA glycosylase                                                                                                                                                                                              SCOP domains
               CATH domains 2uugB00 B:5-226 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                              CATH domains
           Pfam domains (1) ---------------------------------------------UDG-2uugB01 B:50-211                                                                                                                                              --------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------UDG-2uugB02 B:50-211                                                                                                                                              --------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhh..hhhhh..hhh..eeeee........................hhhhhhhhhhh..............hhhhhh.eeeee.................hhhhhhhhhhhhhhh....eeeeehhhhhhhh........eeeee....hhhhhh......hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uug B   5 LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPDPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPA 226
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

Chain C from PDB  Type:PROTEIN  Length:82
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:82
                                    12        22        32        42        52        62        72        82  
           UNGI_BPPB2     3 NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d2uugc_ C: Uracil-DNA glycosylase inhibitor protein                                SCOP domains
               CATH domains 2uugC00 C:3-84  [code=3.10.450.20, no name defined]                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......eeeee.hhhhhhhh.......eeeeeeee....eeeeeeee......eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2uug C   3 NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    12        22        32        42        52        62        72        82

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with UNGI_BPPB2 | P14739 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:82
                                    12        22        32        42        52        62        72        82  
           UNGI_BPPB2     3 NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
               SCOP domains d2uugd_ D: Uracil-DNA glycosylase inhibitor protein                                SCOP domains
               CATH domains 2uugD00 D:3-84  [code=3.10.450.20, no name defined]                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.....eeeeeee.hhhhhhhh.......eeeeeeee....eeeeeeee......eeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2uug D   3 NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML  84
                                    12        22        32        42        52        62        72        82

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

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: UDG (24)

Escherichia coli (strain K12) (7)

1a	UDG-2uugB01	B:50-211
1b	UDG-2uugB02	B:50-211

Asymmetric Unit(hide GO term definitions)

Chain A,B (UNG_ECOLI | P12295)

molecular function
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004844	uracil DNA N-glycosylase activity	Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
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:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain C,D (UNGI_BPPB2 | P14739)

molecular function
	GO:0005515		protein binding		Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2uug)

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	Cis Peptide Bonds
		Ala C:62 - Pro C:63	[ RasMol ]
		Ala D:62 - Pro D:63	[ RasMol ]
		Tyr A:38 - Pro A:39	[ RasMol ]
		Tyr B:38 - Pro B:39	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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(no "Related Entries Specified in the PDB File" available for 2UUG)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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