1EVX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI

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

Date :   20 Apr 00 (Deposition) - 02 Aug 00 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dna Binding B-Sheets; C-Terminal Exchanged Dimer Interface, Hydrolase (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

Molecule 1 - INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PHYSARUM POLYCEPHALUM
	Organism Taxid	:	5791

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:125 , CYS A:132 , HIS A:134 , CYS A:138	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS A:41 , CYS A:100 , CYS A:105 , HIS A:110	BINDING SITE FOR RESIDUE ZN A 1002
3	AC3	SOFTWARE	CYS B:125 , CYS B:132 , HIS B:134 , CYS B:138	BINDING SITE FOR RESIDUE ZN B 1003
4	AC4	SOFTWARE	CYS B:41 , CYS B:100 , CYS B:105 , HIS B:110	BINDING SITE FOR RESIDUE ZN B 1004
5	AC5	SOFTWARE	ARG B:61 , GLY B:76 , SER B:77 , HIS B:78 , THR B:79 , HOH B:1022 , HOH B:1049 , HOH B:1053 , HOH B:1079 , HOH B:1131	BINDING SITE FOR RESIDUE SO4 B 501
6	AC6	SOFTWARE	GLY A:76 , SER A:77 , HIS A:78 , THR A:79 , HOH A:1009 , HOH A:1112 , HOH A:1118	BINDING SITE FOR RESIDUE SO4 A 502
7	AC7	SOFTWARE	THR B:26 , HIS B:28 , THR B:38 , LYS B:65 , VAL B:72 , ARG B:74	BINDING SITE FOR RESIDUE SO4 B 503
8	AC8	SOFTWARE	THR A:26 , HIS A:40 , GLY B:32 , GLY B:33 , GLY B:34 , GLN B:141 , TYR B:145 , HOH B:1149	BINDING SITE FOR RESIDUE SO4 B 504

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:48	-	Pro A:49
2	Ala B:48	-	Pro B:49

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

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

(no "Exon" information available for 1EVX)

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
	(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 d1evxa_ A: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evxA00 A:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...........eee.....eeeeeee..eeeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evx A   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 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 d1evxb_ B: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1evxB00 B:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...........eee.....eeeeeee..eeeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1evx B   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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/Biological 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	d1evxa_	A:
1b	d1evxb_	B:

Asymmetric/Biological 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)

Physarum polycephalum. Organism_taxid: 5791. (1)

1a	1evxA00	A:2-163
1b	1evxB00	B:2-163

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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/Biological Unit
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	Sites
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		AC8	[ RasMol ]	+environment [ RasMol ]

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

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

1a73	WT I-PPOI PRODUCT COMPLEX
1cyq	I-PPOI SUBSTRATE COMPLEX (H98A TRAPPED)
1cz0	I-PPOI SUBSTRATE COMPLEX (SODIUM TRAPPED)
1evw	I-PPOI/DNA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (5, 5)

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