1EVW | PD0140 - 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 :   L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.

Authors :   E. A. Galburt, M. S. Jurica, B. S. Chevalier, D. Erho, B. L. Stoddard

Date :   20 Apr 00 (Deposition) - 03 Aug 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Dna Binding B-Sheets; C-Terminal Exchanged Dimer Interface; Bent Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Galburt, M. S. Chadsey, M. S. Jurica, B. S. Chevalier, D. Erho, W. Tang, R. J. Monnat Jr. , B. L. Stoddard
Conformational Changes And Cleavage By The Homing Endonuclease I-Ppoi: A Critical Role For A Leucine Residue In The Active Site.
J. Mol. Biol. V. 300 877 2000
PubMed-ID: 10891275 | Reference-DOI: 10.1006/JMBI.2000.3874
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(TPGPGPCPTPAPCPCPTPTPAPA)- 3')*
	Chains	:	E, G
	Engineered	:	YES
	Other Details	:	DNA HOMING SITE; STRAND 1
	Other Details - Source	:	SEQUENCE CORRESPONS TO I-PPOI'S HOMING SITE
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(PGPAPGPAPGPTPCPA)-3')*
	Chains	:	M, N
	Engineered	:	YES
	Other Details	:	DNA HOMING SITE; STRAND 2
	Other Details - Source	:	SEQUENCE CORRESPONS TO I-PPOI'S HOMING SITE
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(TPGPAPCPTPCPTPCPTPTPAPA)- 3')*
	Chains	:	F, H
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 4 - DNA (5'-D(PGPGPTPAPGPCPCPA)-3')*
	Chains	:	O, P
	Engineered	:	YES
	Synthetic	:	YES

Molecule 5 - I-PPOI HOMING ENDONUCLEASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PHYSARUM POLYCEPHALUM
	Organism Taxid	:	5791
	Synonym	:	I-PPOI, INTRON-ENCODED ENDONUCLEASE I-PPOI

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	M	N	O	P
Biological Unit 1 (1x)	:	A	B			E	F			M		O
Biological Unit 2 (1x)	:			C	D			G	H		N		P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:125 , CYS A:132 , HIS A:134 , CYS A:138	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	CYS A:41 , CYS A:100 , CYS A:105 , HIS A:110	BINDING SITE FOR RESIDUE ZN A 502
03	AC3	SOFTWARE	CYS B:125 , CYS B:132 , HIS B:134 , CYS B:138	BINDING SITE FOR RESIDUE ZN B 503
04	AC4	SOFTWARE	CYS B:41 , CYS B:100 , CYS B:105 , HIS B:110	BINDING SITE FOR RESIDUE ZN B 504
05	AC5	SOFTWARE	CYS C:125 , CYS C:132 , HIS C:134 , CYS C:138	BINDING SITE FOR RESIDUE ZN C 505
06	AC6	SOFTWARE	CYS C:41 , CYS C:100 , CYS C:105 , HIS C:110	BINDING SITE FOR RESIDUE ZN C 506
07	AC7	SOFTWARE	CYS D:125 , CYS D:132 , HIS D:134 , CYS D:138	BINDING SITE FOR RESIDUE ZN D 507
08	AC8	SOFTWARE	CYS D:41 , CYS D:100 , CYS D:105 , HIS D:110	BINDING SITE FOR RESIDUE ZN D 508
09	AC9	SOFTWARE	HIS C:101 , ASN C:119 , DA H:12 , DG P:13	BINDING SITE FOR RESIDUE MG P 601
10	BC1	SOFTWARE	ASN D:119 , DG N:14	BINDING SITE FOR RESIDUE MG N 602
11	BC2	SOFTWARE	ASN A:119 , DA F:12 , DG O:13	BINDING SITE FOR RESIDUE MG A 603
12	BC3	SOFTWARE	SER B:97 , HIS B:98 , HIS B:101 , ASN B:119 , DG M:14	BINDING SITE FOR RESIDUE MG B 604

(no "SS Bond" information available for 1EVW)

Asymmetric Unit

No.	Residues
1	Ala A:48	-	Pro A:49
2	Ala B:48	-	Pro B:49
3	Ala C:48	-	Pro C:49
4	Ala D:48	-	Pro D:49

(no "SAP(SNP)/Variant" information available for 1EVW)

(no "PROSITE Motif" information available for 1EVW)

(no "Exon" information available for 1EVW)

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:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1evwa_ A: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evwA00 A:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee...........eeeee..eeeeeee....eeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evw A   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESADDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1evwb_ B: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evwB00 B:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee...........eeeee..eeeeeeee..eeeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evw B   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESADDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1evwc_ C: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evwC00 C:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee...........eeeee..eeeeeee....eeeee..hhhhh....ee..eeeee..........hhhhh.eeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evw C   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESADDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1evwd_ D: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evwD00 D:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...........eeeee..eeeeeee....eeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evw D   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESADDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain E from PDB  Type:DNA  Length:12
                                            
                 1evw E   2 TGGCTACCTTAA  13
                                    11

Chain F from PDB  Type:DNA  Length:12
                                            
                 1evw F   1 TGACTCTCTTAA  12
                                    10

Chain G from PDB  Type:DNA  Length:12
                                            
                 1evw G   2 TGGCTACCTTAA  13
                                    11

Chain H from PDB  Type:DNA  Length:12
                                            
                 1evw H   1 TGACTCTCTTAA  12
                                    10

Chain M from PDB  Type:DNA  Length:8
                                        
                 1evw M  14 GAGAGTCA  21

Chain N from PDB  Type:DNA  Length:8
                                        
                 1evw N  14 GAGAGTCA  21

Chain O from PDB  Type:DNA  Length:8
                                        
                 1evw O  13 GGTAGCCA  20

Chain P from PDB  Type:DNA  Length:8
                                        
                 1evw P  13 GGTAGCCA  20

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: His-Me finger endonucleases (64)

Superfamily: His-Me finger endonucleases (64)

Family: Intron-encoded homing endonucleases (9)

Protein domain: Intron-encoded homing endonuclease I-PpoI (8)

Slime mold (Physarum polycephalum) [TaxId: 5791] (8)

1a	d1evwa_	A:
1b	d1evwb_	B:
1c	d1evwc_	C:
1d	d1evwd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A (8)

Homologous Superfamily: Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A (8)

[unclassified] (6)

1a	1evwA00	A:2-163
1b	1evwB00	B:2-163
1c	1evwC00	C:2-163
1d	1evwD00	D:2-163

(no "Pfam Domain" information available for 1EVW)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PPO1_PHYPO | Q94702)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0006314	intron homing	Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Ala A:48 - Pro A:49	[ RasMol ]
		Ala B:48 - Pro B:49	[ RasMol ]
		Ala C:48 - Pro C:49	[ RasMol ]
		Ala D:48 - Pro D:49	[ RasMol ]

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

Jmol
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	1evw
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	PPO1_PHYPO \| Q94702
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UniProtKB/Swiss-Prot
	PPO1_PHYPO \| Q94702	:	1a73 1a74 1cyq 1cz0 1evx 1ipp 2o6m

1a73	WILD-TYPE I-PPOI COMPLEXED TO DNA HOMING SITE (PRODUCT COMPLEX)
1cyq	I-PPOI SUBSTRATE COMPLEX (H98A TRAPPED)
1cz0	I-PPOI SUBSTRATE COMPLEX (SODIUM TRAPPED)
1evx	APO STRUCTURE OF I-PPOI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (1, 4)

CATH Domains (1, 4)

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