4IEM - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE (APE1) WITH PRODUCT DNA AND MG2+

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

Date :   13 Dec 12 (Deposition) - 23 Jan 13 (Release) - 10 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,E,F,G  (1x)
Biol. Unit 2: B,H,I,J  (1x)
Biol. Unit 3: C,K,L,M  (1x)
Biol. Unit 4: D,N,O,P  (1x)

Keywords :   Metalloprotein, Dna Damage, Dna Repair, Base Excision Repair, Protein-Dna, Ref1, Nuclease, Hydrolase, Lyase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Tsutakawa, D. S. Shin, C. D. Mol, T. Izumi, A. S. Arvai, A. K. Mantha B. Szczesny, I. N. Ivanov, D. J. Hosfield, B. Maiti, M. E. Pique, K. A. Frankel, K. Hitomi, R. P. Cunningham, S. Mitra, J. A. Tainer
Conserved Structural Chemistry For Incision Activity In Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease Ape1 And Endonuclease Iv Dna Repair Enzymes.
J. Biol. Chem. V. 288 8445 2013
PubMed-ID: 23355472 | Reference-DOI: 10.1074/JBC.M112.422774

Molecule 1 - DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.-.-, 4.2.99.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	APE, APE1, APEX, APEX1, APX, HAP1, REF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APEX NUCLEASE, APEN, APURINIC-APYRIMIDINIC ENDONUCLEASE 1, AP ENDONUCLEASE 1, APE-1, REF-1, REDOX FACTOR-1, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, MITOCHONDRIAL

*Molecule 2 - DNA (5'-D(GPCPTPAPC)-3')**
	Chains	:	E, H, K, N
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC DNA
	Organism Taxid	:	32630
	Other Details	:	DNA OLIGONUCLEOTIDE SYNTHESIS
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(P(3DR)PGPAPTPCPG)-3')*
	Chains	:	F, I, L, O
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC DNA
	Organism Taxid	:	32630
	Other Details	:	DNA OLIGONUCLEOTIDE SYNTHESIS
	Synthetic	:	YES

*Molecule 4 - DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3')**
	Chains	:	G, J, M, P
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC DNA
	Organism Taxid	:	32630
	Other Details	:	DNA OLIGONUCLEOTIDE SYNTHESIS
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P
Biological Unit 1 (1x)	:	A				E	F	G
Biological Unit 2 (1x)	:		B						H	I	J
Biological Unit 3 (1x)	:			C								K	L	M
Biological Unit 4 (1x)	:				D										N	O	P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	3DR	4	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MG	7	Ligand/Ion	MAGNESIUM ION
3	NA	9	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:641 , DC E:505 , DG G:518 , DT G:519 , HOH G:606	BINDING SITE FOR RESIDUE MG A 501
02	AC2	SOFTWARE	GLU A:96 , HOH A:601 , HOH A:602 , HOH A:603 , DC E:505 , 3DR F:506	BINDING SITE FOR RESIDUE MG A 502
03	AC3	SOFTWARE	DT L:509 , DT M:515	BINDING SITE FOR RESIDUE MG A 503
04	AC4	SOFTWARE	TYR A:269 , MET A:270 , MET A:271 , ASN A:272 , DG G:518	BINDING SITE FOR RESIDUE NA A 504
05	AC5	SOFTWARE	LEU A:44 , TYR A:45	BINDING SITE FOR RESIDUE NA A 505
06	AC6	SOFTWARE	GLU B:96 , HOH B:502 , HOH B:503 , DC H:505 , 3DR I:506 , HOH I:601	BINDING SITE FOR RESIDUE MG B 401
07	AC7	SOFTWARE	ASP B:47 , TYR B:257 , SER B:298 , LYS B:299	BINDING SITE FOR RESIDUE NA B 402
08	AC8	SOFTWARE	ARG B:185 , ASP B:189 , VAL B:213 , GLU B:236	BINDING SITE FOR RESIDUE NA B 403
09	AC9	SOFTWARE	ASP B:189 , ARG B:193 , LEU B:243	BINDING SITE FOR RESIDUE NA B 404
10	BC1	SOFTWARE	GLU C:96 , HOH C:601 , HOH C:602 , DC K:505 , HOH K:701 , 3DR L:506	BINDING SITE FOR RESIDUE MG C 401
11	BC2	SOFTWARE	ASP C:70 , HOH C:614 , HOH C:668 , DC K:505 , HOH K:701 , DG M:518 , DT M:519	BINDING SITE FOR RESIDUE MG C 402
12	BC3	SOFTWARE	GLU D:96 , HOH D:501 , HOH D:502 , DC N:505 , HOH N:701 , 3DR O:506	BINDING SITE FOR RESIDUE MG D 401
13	BC4	SOFTWARE	ASN D:222 , DT O:509	BINDING SITE FOR RESIDUE NA D 402
14	BC5	SOFTWARE	DT E:503 , DA E:504	BINDING SITE FOR RESIDUE NA E 601
15	BC6	SOFTWARE	DC F:510	BINDING SITE FOR RESIDUE NA F 601
16	BC7	SOFTWARE	DT N:503 , DA N:504	BINDING SITE FOR RESIDUE NA N 601

(no "SS Bond" information available for 4IEM)

Asymmetric Unit

No.	Residues
1	Val A:247	-	Pro A:248
2	Val B:247	-	Pro B:248
3	Val C:247	-	Pro C:248
4	Val D:247	-	Pro D:248

(no "SAP(SNP)/Variant" information available for 4IEM)

(no "PROSITE Motif" information available for 4IEM)

(no "Exon" information available for 4IEM)

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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....eeeee..........eeeee.....eeee...hhhhh....eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh...........hhhhh.........eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iem A  41 GPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhheeeee..........eeeee.....eeee............eeeee....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhh....eehhhhhh...............hhhhh.....eeeee.hhhh..eeee.............eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iem B  44 LYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....eeeee..........eeeee.....eeee...hhhhh....eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh...........hhhhhhhhh.....eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iem C  41 GPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain D from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhheeeee..........eeeee.....eeee............eeeee....eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh.eeehhhhhh...........hhhhh.........eeeeee.hhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iem D  43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain E from PDB  Type:DNA  Length:5
                                     
                 4iem E 501 GCTAC 505

Chain F from PDB  Type:DNA  Length:6
                                      
                 4iem F 506 xGATCG 511
                            |     
                          506-3DR

Chain G from PDB  Type:DNA  Length:11
                                           
                 4iem G 512 CGATCGGTAGC 522
                                   521

Chain H from PDB  Type:DNA  Length:5
                                     
                 4iem H 501 GCTAC 505

Chain I from PDB  Type:DNA  Length:5
                                     
                 4iem I 506 xGATC 510
                            |    
                          506-3DR

Chain J from PDB  Type:DNA  Length:11
                                           
                 4iem J 512 CGATCGGTAGC 522
                                   521

Chain K from PDB  Type:DNA  Length:5
                                     
                 4iem K 501 GCTAC 505

Chain L from PDB  Type:DNA  Length:6
                                      
                 4iem L 506 xGATCG 511
                            |     
                          506-3DR

Chain M from PDB  Type:DNA  Length:11
                                           
                 4iem M 512 CGATCGGTAGC 522
                                   521

Chain N from PDB  Type:DNA  Length:5
                                     
                 4iem N 501 GCTAC 505

Chain O from PDB  Type:DNA  Length:6
                                      
                 4iem O 506 xGATCG 511
                            |     
                          506-3DR

Chain P from PDB  Type:DNA  Length:11
                                           
                 4iem P 512 CGATCGGTAGC 522
                                   521

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4IEM)

(no "CATH Domain" information available for 4IEM)

(no "Pfam Domain" information available for 4IEM)

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	Cis Peptide Bonds
		Val A:247 - Pro A:248	[ RasMol ]
		Val B:247 - Pro B:248	[ RasMol ]
		Val C:247 - Pro C:248	[ RasMol ]
		Val D:247 - Pro D:248	[ RasMol ]

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	4iem
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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