1FSJ - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN

Authors :   U. C. Kuhlmann, A. J. Pommer, G. R. Moore, R. James, C. Kleanthous, A. M. Hemmings

Date :   11 Sep 00 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : B,C,D,E
Biol. Unit 1: B  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: D  (1x)
Biol. Unit 4: E  (1x)

Keywords :   Zinc Containing Enzyme, Hnh-Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. C. Kuhlmann, A. J. Pommer, G. R. Moore, R. James, C. Kleanthous, A. M. Hemmings
Structure Of The E9 Dnase Domain In Comparison With The Inhibited Structure Of The E9 Dnase/Im9 Complex
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - COLICIN E9
	Chains	:	B, C, D, E
	EC Number	:	3.1.21.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21D (PRJ353)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN OF E9 COLICIN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION
2	ZN	4	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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:5 , LEU B:101 , HIS B:102 , HIS B:103 , HIS B:127 , HIS B:131 , ZN B:901 , HOH B:932 , HOH B:973	BINDING SITE FOR RESIDUE PO4 B 801
2	AC2	SOFTWARE	ARG C:205 , HIS C:302 , HIS C:303 , HIS C:327 , ZN C:902 , HOH C:908 , HOH C:937 , LYS E:734	BINDING SITE FOR RESIDUE PO4 C 802
3	AC3	SOFTWARE	LYS B:134 , HOH D:28 , HOH D:43 , HOH D:111 , ARG D:405 , HIS D:502 , HIS D:503 , HIS D:527 , ZN D:903	BINDING SITE FOR RESIDUE PO4 D 803
4	AC4	SOFTWARE	HOH E:31 , HOH E:298 , ARG E:605 , LEU E:701 , HIS E:702 , HIS E:703 , HIS E:727 , HIS E:731 , ZN E:904	BINDING SITE FOR RESIDUE PO4 E 804
5	AC5	SOFTWARE	HIS B:102 , HIS B:127 , HIS B:131 , PO4 B:801 , HOH B:932	BINDING SITE FOR RESIDUE ZN B 901
6	AC6	SOFTWARE	HIS C:302 , HIS C:327 , HIS C:331 , PO4 C:802 , HOH C:911	BINDING SITE FOR RESIDUE ZN C 902
7	AC7	SOFTWARE	HOH D:28 , HIS D:502 , HIS D:527 , HIS D:531 , PO4 D:803	BINDING SITE FOR RESIDUE ZN D 903
8	AC8	SOFTWARE	HOH E:31 , HIS E:702 , HIS E:727 , HIS E:731 , PO4 E:804	BINDING SITE FOR RESIDUE ZN E 904

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

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

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

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

(no "Exon" information available for 1FSJ)

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 B from PDB  Type:PROTEIN  Length:134
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:134
                                   458       468       478       488       498       508       518       528       538       548       558       568       578    
           CEA9_ECOLX   449 KESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1fsjb_ B: DNase domain of colicin E9                                                                                                  SCOP domains
               CATH domains 1fsjB00 B:1-134 Colicin e7 immunity protein. Chain B                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.ee..........hhhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fsj B   1 MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   460       470       480       490       500       510       520       530       540       550       560       570       580  
           CEA9_ECOLX   451 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1fsjc_ C: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1fsjC00 C:203-334 Colicin e7 immunity protein. Chain B                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fsj C 203 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 334
                                   212       222       232       242       252       262       272       282       292       302       312       322       332

Chain D from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   460       470       480       490       500       510       520       530       540       550       560       570       580  
           CEA9_ECOLX   451 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1fsjd_ D: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1fsjD00 D:403-534 Colicin e7 immunity protein. Chain B                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fsj D 403 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 534
                                   412       422       432       442       452       462       472       482       492       502       512       522       532

Chain E from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   460       470       480       490       500       510       520       530       540       550       560       570       580  
           CEA9_ECOLX   451 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1fsje_ E: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1fsjE00 E:603-734 Colicin e7 immunity protein. Chain B                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.ee..........hhhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhh.......hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fsj E 603 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 734
                                   612       622       632       642       652       662       672       682       692       702       712       722       732

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(

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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: HNH-motif (35)

Protein domain: DNase domain of colicin E9 (15)

Escherichia coli [TaxId: 562] (15)

1a	d1fsjb_	B:
1b	d1fsjc_	C:
1c	d1fsjd_	D:
1d	d1fsje_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain (34)

Homologous Superfamily: Colicin e7 immunity protein. Chain B (34)

Escherichia coli. Organism_taxid: 562. (11)

1a	1fsjC00	C:203-334
1b	1fsjD00	D:403-534
1c	1fsjE00	E:603-734
1d	1fsjB00	B:1-134

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

Asymmetric Unit(hide GO term definitions)

Chain B,C,D,E (CEA9_ECOLX | P09883)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fsj)

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1bxi	1BXI IS E9 DNASE DOMAIN COMPLEXED WITH INHIBITOR IM9
1emv	1EMV IS METAL FREE E9 DNASE/IM9 COMPLEX
1fr2	1FR2 IS E9 DNASE COMPLEXED WITH MUTANT IM9(E41A)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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