1KHO - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN ISOLATED FROM AVIAN STRAIN SWCP

Authors :   N. Justin, D. S. Moss, R. W. Titball, A. K. Basak

Date :   30 Nov 01 (Deposition) - 19 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   N-Terminal Alpha-Helix, C-Terminal Beta-Sheet, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Justin, N. Walker, H. L. Bullifent, G. Songer, D. M. Bueschel, H. Jost, C. Naylor, J. Miller, D. S. Moss, R. W. Titball, A. K. Basak
The First Strain Of Clostridium Perfringens Isolated From An Avian Source Has An Alpha-Toxin With Divergent Structural And Kinetic Properties.
Biochemistry V. 41 6253 2002
PubMed-ID: 12009886 | Reference-DOI: 10.1021/BI012015V
(for further references see the PDB file header)

Molecule 1 - ALPHA-TOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	CPA
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:1 , HIS A:11 , ASP A:130 , ZN A:372 , HOH A:421	BINDING SITE FOR RESIDUE ZN A 371
2	AC2	SOFTWARE	ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:371 , HOH A:421	BINDING SITE FOR RESIDUE ZN A 372
3	AC3	SOFTWARE	HIS A:136 , HIS A:148 , GLU A:152 , HOH A:374	BINDING SITE FOR RESIDUE ZN A 373
4	AC4	SOFTWARE	TRP B:1 , HIS B:11 , ASP B:130 , ZN B:375 , HOH B:424	BINDING SITE FOR RESIDUE ZN B 374
5	AC5	SOFTWARE	ASP B:56 , HIS B:68 , HIS B:126 , ASP B:130 , ZN B:374 , HOH B:424	BINDING SITE FOR RESIDUE ZN B 375
6	AC6	SOFTWARE	HIS B:136 , HIS B:148 , GLU B:152 , HOH B:377	BINDING SITE FOR RESIDUE ZN B 376

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROKAR_ZN_DEPEND_PLPC_1	PS00384	Prokaryotic zinc-dependent phospholipase C signature.	PHLC_CLOPF	154-167	2	A:126-139 B:126-139
2	PLAT	PS50095	PLAT domain profile.	PHLC_CLOPF	284-398	2	A:256-370 B:256-370

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROKAR_ZN_DEPEND_PLPC_1	PS00384	Prokaryotic zinc-dependent phospholipase C signature.	PHLC_CLOPF	154-167	1	A:126-139 -
2	PLAT	PS50095	PLAT domain profile.	PHLC_CLOPF	284-398	1	A:256-370 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROKAR_ZN_DEPEND_PLPC_1	PS00384	Prokaryotic zinc-dependent phospholipase C signature.	PHLC_CLOPF	154-167	1	- B:126-139
2	PLAT	PS50095	PLAT domain profile.	PHLC_CLOPF	284-398	1	- B:256-370

(no "Exon" information available for 1KHO)

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:370
 aligned with PHLC_CLOPF | Q9RF12 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:370
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398
           PHLC_CLOPF    29 WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK 398
               SCOP domains d1khoa1 A:1-249 Alpha-toxin, N-terminal domain                                                                                                                                                                                                           d1khoa2 A:250-370 Alpha-toxin, C-terminal domain                                                                          SCOP domains
               CATH domains 1khoA01 A:1-250 P1 Nuclease                                                                                                                                                                                                                               1khoA02 A:251-370 Lipoxygenase-1                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeee..........eeeeeeee....eeeee............eeeeeee......hhh.eeeeeeeee..........eeeeeeee..eeeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PROKAR_ZN_DEPE--------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:256-370 UniProt: 284-398                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kho A   1 WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK 370
                                    10        20        30        40        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       320       330       340       350       360       370

Chain B from PDB  Type:PROTEIN  Length:370
 aligned with PHLC_CLOPF | Q9RF12 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:370
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398
           PHLC_CLOPF    29 WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK 398
               SCOP domains d1khob1 B:1-249 Alpha-toxin, N-terminal domain                                                                                                                                                                                                           d1khob2 B:250-370 Alpha-toxin, C-terminal domain                                                                          SCOP domains
               CATH domains 1khoB01 B:1-250 P1 Nuclease                                                                                                                                                                                                                               1khoB02 B:251-370 Lipoxygenase-1                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeee..........eeeeeeee....eeeee............eeeeeee......hhh.eeeeeeeee..........eeeeeeee..eeeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PROKAR_ZN_DEPE--------------------------------------------------------------------------------------------------------------------PLAT  PDB: B:256-370 UniProt: 284-398                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kho B   1 WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK 370
                                    10        20        30        40        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       320       330       340       350       360       370

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: P1 Nuclease (17)

Homologous Superfamily: P1 Nuclease (17)

Clostridium perfringens. Organism_taxid: 1502. (1)

1a	1khoA01	A:1-250
1b	1khoB01	B:1-250

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Lipoxygenase-1 (46)

Homologous Superfamily: Lipoxygenase-1 (44)

Clostridium perfringens. Organism_taxid: 1502. (1)

2a	1khoA02	A:251-370
2b	1khoB02	B:251-370

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHLC_CLOPF | Q9RF12)

molecular function
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0034480	phosphatidylcholine phospholipase C activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1,2-diacylglycerol + a choline phosphate.
	GO:0004629	phospholipase C activity	Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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1ca1	ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS
1qm6	R32 FORM OF CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN
1qmd	CALCIUM BOUND CLOSED FORM ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS

Description

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Ligands, Modified Residues, Ions (1, 6)

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SS Bonds (0, 0)

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