1MZ8 - JenaLib

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Title :   CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION

Authors :   M. J. Sui, L. C. Tsai, K. C. Hsia, L. G. Doudeva, W. Y. Ku, G. W. Han, H. S. Yuan

Date :   07 Oct 02 (Deposition) - 23 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   H-N-H Motif, Toxin, Hydrolase/Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Sui, L. C. Tsai, K. C. Hsia, L. G. Doudeva, W. Y. Ku, G. W. Han, H. S. Yuan
Metal Ions And Phosphate Binding In The H-N-H Motif: Crystal Structures Of The Nuclease Domain Of Cole7/Im7 In Complex With A Phosphate Ion And Different Divalent Metal Ions
Protein Sci. V. 11 2947 2002
PubMed-ID: 12441392 | Reference-DOI: 10.1110/PS.0220602
(for further references see the PDB file header)

Molecule 1 - COLICIN E7 IMMUNITY PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CEI7
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - COLICIN E7
	Chains	:	B, D
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEASE DOMAIN
	Gene	:	CEA7
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:544 , HIS B:569 , HIS B:573 , PO4 B:601	BINDING SITE FOR RESIDUE ZN B 600
2	AC2	SOFTWARE	ARG B:447 , HIS B:544 , HIS B:545 , HIS B:569 , HIS B:573 , ZN B:600	BINDING SITE FOR RESIDUE PO4 B 601
3	AC3	SOFTWARE	HIS D:544 , HIS D:569 , HIS D:573 , PO4 D:601	BINDING SITE FOR RESIDUE ZN D 600
4	AC4	SOFTWARE	ARG D:447 , HIS D:544 , HIS D:545 , HIS D:569 , HIS D:573 , ZN D:600 , HOH D:1033	BINDING SITE FOR RESIDUE PO4 D 601

(no "SS Bond" information available for 1MZ8)

(no "Cis Peptide Bond" information available for 1MZ8)

(no "SAP(SNP)/Variant" information available for 1MZ8)

(no "PROSITE Motif" information available for 1MZ8)

(no "Exon" information available for 1MZ8)

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:87
 aligned with IMM7_ECOLX | Q03708 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           IMM7_ECOLX     1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
               SCOP domains d1mz8a_ A: ImmE7 protein (Im7)                                                          SCOP domains
               CATH domains 1mz8A00 A:1-87  [code=1.10.1200.20, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1mz8 A   1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:131
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d1mz8b_ B: DNase domain of colicin E7                                                                                               SCOP domains
               CATH domains 1mz8B00 B:446-576 Colicin e7 immunity protein. Chain B                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mz8 B 446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   455       465       475       485       495       505       515       525       535       545       555       565       575

Chain C from PDB  Type:PROTEIN  Length:87
 aligned with IMM7_ECOLX | Q03708 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           IMM7_ECOLX     1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
               SCOP domains d1mz8c_ C: ImmE7 protein (Im7)                                                          SCOP domains
               CATH domains 1mz8C00 C:1-87  [code=1.10.1200.20, no name defined]                                    CATH domains
           Pfam domains (1) Colicin_Pyocin-1mz8C01 C:1-86                                                         - Pfam domains (1)
           Pfam domains (2) Colicin_Pyocin-1mz8C02 C:1-86                                                         - Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1mz8 C   1 MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQG  87
                                    10        20        30        40        50        60        70        80

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:130
                                   456       466       476       486       496       506       516       526       536       546       556       566       576
           CEA7_ECOLX   447 RNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d1mz8d_ D: DNase domain of colicin E7                                                                                              SCOP domains
               CATH domains 1mz8D00 D:447-576 Colicin e7 immunity protein. Chain B                                                                             CATH domains
           Pfam domains (1) Colicin-DNase-1mz8D01 D:447-575                                                                                                  - Pfam domains (1)
           Pfam domains (2) Colicin-DNase-1mz8D02 D:447-575                                                                                                  - Pfam domains (2)
         Sec.struct. author ....ee.....................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mz8 D 447 RNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   456       466       476       486       496       506       516       526       536       546       556       566       576

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: His-Me_finger (38)

Family: Colicin-DNase (14)

Escherichia coli (14)

1a	Colicin-DNase-1mz8D01	D:447-575
1b	Colicin-DNase-1mz8D02	D:447-575

Clan: no clan defined [family: Colicin_Pyocin] (11)

Family: Colicin_Pyocin (11)

Escherichia coli (11)

2a	Colicin_Pyocin-1mz8C01	C:1-86
2b	Colicin_Pyocin-1mz8C02	C:1-86

Asymmetric Unit(hide GO term definitions)

Chain A,C (IMM7_ECOLX | Q03708)

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).
	GO:0015643	toxic substance binding	Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
	GO:0030153	bacteriocin immunity	A process that mediates resistance to a bacteriocin: any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary.

Chain B,D (CEA7_ECOLX | Q47112)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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).
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005727	extrachromosomal circular DNA	Circular DNA structures that are not part of a chromosome.

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7cei	7CEI CONTAINS THE ENDONUCLEASE DOMAIN OF COLICIN E7 COMPLEXED WITH ITS INHIBITOR IM7 PROTEIN

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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