5T4I - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   A NOVEL DOMAIN IN HUMAN EXOG CONVERTS APOPTOTIC ENDONUCLEASE TO DNA-REPAIR ENZYME

Authors :   M. R. Szymanski, W. Y. Yin

Date :   29 Aug 16 (Deposition) - 17 May 17 (Release) - 17 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Mitochondria, Exonuclease, Dna-Repair, Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Szymanski, W. Yu, A. M. Gmyrek, M. A. White, I. J. Molineux, J. C. Lee, Y. W. Yin
A Domain In Human Exog Converts Apoptotic Endonuclease To Dna-Repair Exonuclease.
Nat Commun V. 8 14959 2017
PubMed-ID: 28466855 | Reference-DOI: 10.1038/NCOMMS14959

Molecule 1 - NUCLEASE EXOG, MITOCHONDRIAL
	Chains	:	A, B
	EC Number	:	3.1.30.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 59-358
	Gene	:	EXOG, ENDOGL1, ENDOGL2, ENGL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDONUCLEASE G-LIKE 1,ENDO G-LIKE 1

*Molecule 2 - DNA (5'-D(PCPTPGPAPCPGPTPGPC)-3')**
	Chains	:	C, E
	Engineered	:	YES
	Organism Scientific	:	DNA LAUNCH VECTOR PDE-GFP2
	Organism Taxid	:	415098
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(GPCPAPCPGPTPCPAPG)-3')**
	Chains	:	D, F
	Engineered	:	YES
	Organism Scientific	:	DNA LAUNCH VECTOR PDE-GFP2
	Organism Taxid	:	415098
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:171 , HOH A:509 , DT E:2 , DG E:3	binding site for residue MN A 401
2	AC2	SOFTWARE	ASN B:171 , HOH B:501 , HOH B:502 , HOH B:507 , DT C:2 , DG C:3	binding site for residue MN B 401

Asymmetric/Biological Unit

No.	Residues
1	A:294	-	A:299
2	B:294	-	B:299

Asymmetric/Biological Unit

No.	Residues
1	Asn A:334	-	Ala A:335
2	Asp A:340	-	Asp A:341

(no "SAP(SNP)/Variant" information available for 5T4I)

(no "PROSITE Motif" information available for 5T4I)

(no "Exon" information available for 5T4I)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..........ee...eeeeee....eeeeeeeee.........hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eee.....eeeeeeee....ee...eeeeeeeee........eeeeeeeee........hhhh.eehhhhhhhhhh............eeehhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t4i A  60 AVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGAMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDYFMSRYEKKLEELKA 356
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349

Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eee...eeeeee....eeeeeeeee.hhhhh...hhhhh........hhhhh.hhhhhh....eeee..hhhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...ee.....eeeeeeee....ee...eeeeeeeee........eeeeeeeee........hhhh.eehhhhhhhhhh............eeehhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t4i B  60 AVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGAMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDYFMSRYEKKLEELKAK 357
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349

Chain C from PDB  Type:DNA  Length:9
                                         
                 5t4i C   1 CTGACGTGC   9

Chain D from PDB  Type:DNA  Length:9
                                         
                 5t4i D   2 GCACGTCAG  10

Chain E from PDB  Type:DNA  Length:9
                                         
                 5t4i E   1 CTGACGTGC   9

Chain F from PDB  Type:DNA  Length:9
                                         
                 5t4i F   2 GCACGTCAG  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 '\|'

(no "SCOP Domain" information available for 5T4I)

(no "CATH Domain" information available for 5T4I)

(no "Pfam Domain" information available for 5T4I)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:334 - Ala A:335	[ RasMol ]
		Asp A:340 - Asp A:341	[ RasMol ]

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	5t4i
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	3.1.30.-
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	EXOG_HUMAN \| Q9Y2C4	:	4a1n 5t3v 5t40 5t5c

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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