2WXT - JenaLib

Title :   CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237

Authors :   N. Justin, C. E. Naylor, A. K. Basak

Date :   10 Nov 09 (Deposition) - 17 Nov 09 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Cytolysis, Hydrolase, Hemolysis, Membrane Binding, Gangrene Determinant, C2 Domain, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Vachieri, G. C. Clark, A. Alape-Giron, M. Flores-Diaz, N. Justin, C. E. Naylor, R. W. Titball, A. K. Basak
Comparison Of A Nontoxic Variant Of Clostridium Perfringens [Alpha]-Toxin With The Toxic Wild-Type Strain
Acta Crystallogr. , Sect. D V. 66 1067 2010
PubMed-ID: 20944240 | Reference-DOI: 10.1107/S090744491003369X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:1 , HIS A:11 , ASP A:130 , CD A:1373 , HOH A:2243	BINDING SITE FOR RESIDUE ZN A1371
02	AC2	SOFTWARE	HIS A:46 , GLU A:47 , GLU A:359	BINDING SITE FOR RESIDUE CD A1372
03	AC3	SOFTWARE	ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:1371 , HOH A:2065 , HOH A:2243	BINDING SITE FOR RESIDUE CD A1373
04	AC4	SOFTWARE	HIS A:136 , HIS A:148 , GLU A:152	BINDING SITE FOR RESIDUE CD A1374
05	AC5	SOFTWARE	GLU A:157 , HOH A:2118	BINDING SITE FOR RESIDUE CD A1375
06	AC6	SOFTWARE	GLY A:168 , CYS A:169 , HIS A:207 , HOH A:2124 , HOH A:2156	BINDING SITE FOR RESIDUE CD A1376
07	AC7	SOFTWARE	CYS A:169 , GLU A:173 , ASP A:216 , HOH A:2125 , HOH A:2160	BINDING SITE FOR RESIDUE CD A1377
08	AC8	SOFTWARE	GLU A:173 , HIS A:212 , ASP A:216 , HOH A:2154 , HOH A:2159	BINDING SITE FOR RESIDUE CD A1378
09	AC9	SOFTWARE	HIS A:241 , GLU A:245	BINDING SITE FOR RESIDUE CD A1379
10	BC1	SOFTWARE	ASP A:273 , ASN A:297 , HOH A:2190	BINDING SITE FOR RESIDUE CA A1380
11	BC2	SOFTWARE	ASP A:293	BINDING SITE FOR RESIDUE CA A1381

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:360
 aligned with PHLC_CLOP1 | Q0TV31 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_CLOP1    29 WDGKIDGTGTHAMIVTQGVSILENDLSKNEPESVRKNLEILKENMHELQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFSKDNSWYLAYSIPDTGESQIRKFSALARYEWQRGNYKQATFYLGEAMHYFGDIDTPYHPANVTAVDSAGHVKFETFAEERKEQYKINTAGCKTNEAFYTDILKNKDFNAWSKEYARGFAKTGKSIYYSHASMSHSWDDWDYAAKVTLANSQKGTAGYIYRFLHDVSEGNDPSVGKNVKELVAYISTSGEKDAGTDDYMYFGIKTKDGKTQEWEMDNPGNDFMTGSKDTYTFKLKDENLKIDDIQNMWIRKRKYTAFSDAYKPENIKIIANGKVVVDKDINEWISGNSTYNIK 398
               SCOP domains d2wxta1 A:1-249 Alpha-toxin, N-terminal domain                                                                                                                                                                                                           d2wxta2 A:250-370 Alpha-toxin, C-terminal domain                                                                          SCOP domains
               CATH domains 2wxtA01 A:1-250 P1 Nuclease                                                                                                                                                                                                                               2wxtA02 A:251-370 Lipoxygenase-1                                                                                         CATH domains
               Pfam domains ---------Zn_dep_PLPC-2wxtA02 A:10-227                                                                                                                                                                                              ------------------------------PLAT-2wxtA01 A:258-370                                                                                            Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh......----------.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee..........eeeeeeee....eeeee............eeeeeee......hhh.eeeeeeeee..........eeeeeeee..eeeeeee.........eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PROKAR_ZN_DEPE--------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:256-370 UniProt: 284-398                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wxt A   1 WDGKIDGTGTHAMIVTQGVSILENDLSKNEPESVRKNLEILKENMHELQLGSTYPDYDKNAYDLYQDHFWDPDTD----------LAYSIPDTGESQIRKFSALARYEWQRGNYKQATFYLGEAMHYFGDIDTPYHPANVTAVDSAGHVKFETFAEERKEQYKINTAGCKTNEAFYTDILKNKDFNAWSKEYARGFAKTGKSIYYSHASMSHSWDDWDYAAKVTLANSQKGTAGYIYRFLHDVSEGNDPSVGKNVKELVAYISTSGEKDAGTDDYMYFGIKTKDGKTQEWEMDNPGNDFMTGSKDTYTFKLKDENLKIDDIQNMWIRKRKYTAFSDAYKPENIKIIANGKVVVDKDINEWISGNSTYNIK 370
                                    10        20        30        40        50        60        70    |    -     |  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
                                                                                                     75         86

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PHLC_CLOP1 | Q0TV31)

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.

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