3QIX - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BONT/A LC WITH ZINC BOUND

Authors :   A. A. Thompson, G. W. Han, R. C. Stevens

Date :   28 Jan 11 (Deposition) - 13 Apr 11 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.41

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

Keywords :   Botulinum, Bont, Neurotoxin, Toxin, Metalloprotease, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Thompson, G. S. Jiao, S. Kim, A. Thai, L. Cregar-Hernandez, S. A. Margosiak, A. T. Johnson, G. W. Han, S. O'Malley, R. C. Stevens
Structural Characterization Of Three Novel Hydroxamate-Base Zinc Chelating Inhibitors Of The Clostridium Botulinum Serotype A Neurotoxin Light Chain Metalloprotease Reveals A Compact Binding Site Resulting From 60/70 Loop Flexibility.
Biochemistry V. 50 4019 2011
PubMed-ID: 21434688 | Reference-DOI: 10.1021/BI2001483

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
	Chains	:	A, B
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGHT CHAIN (UNP RESIDUES 3-424)
	Gene	:	BOTA, CBO0806, CLC_0862, NEUROTOXIN LIGHT CHAIN
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	441771
	Strain	:	HALL - SEROTYPE A
	Synonym	:	BONT/A, BONTOXILYSIN-A, BOTOX

		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 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:375 , MET A:411 , THR A:414	BINDING SITE FOR RESIDUE EDO A 700
2	AC2	SOFTWARE	HIS A:223 , HIS A:227 , GLU A:262 , HOH A:606	BINDING SITE FOR RESIDUE ZN A 1001
3	AC3	SOFTWARE	HIS B:223 , HIS B:227 , GLU B:262 , HOH B:607	BINDING SITE FOR RESIDUE ZN B 1002

(no "SS Bond" information available for 3QIX)

Asymmetric Unit

No.	Residues
1	Val A:68	-	Pro A:69

(no "SAP(SNP)/Variant" information available for 3QIX)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	2	A:220-229 B:220-229

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	1	A:220-229 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	1	- B:220-229

(no "Exon" information available for 3QIX)

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:396
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:419
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
           BXA1_CLOBH     2 PFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFT 420
               SCOP domains d3qixa_ A: automated matc hes                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...-.....eeeeeee..eeeeeee........-......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeeee..-----------.eee.hhhhhhhhhhhhhhhhhh........ee...----------.eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhheee.....eeehhhhhhhhhhhhhh..hhhhhhhhhh.............eee...................hhhhh.hhhhh...hhhhheee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qix A   2 GFVNKQFNYKDPVNGVDIAYIKIPN-GQMQPVKAFKIHNKIWVIPERDTFTNPEE-DLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEES-----------GKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVN----------EVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFT 420
                                    11        21    | | 31        41        51    | | 61        71        81        91       101       111       121       131       141       151       161       171       181       191       | -       211       221       231       241    |    -     | 261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
                                                   26 |                          56 |                                                                                                                                          199         211                                246        257                                                                                                                                                                   
                                                     28                            58

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:418
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411        
           BXA1_CLOBH     2 PFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNF 419
               SCOP domains d3qixb_ B: automated matc hes                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peptidase_M27-3qixB01 B: 3-410                                                                                                                                                                                                                                                                                                                                                                                          --------- Pfam domains (1)
           Pfam domains (2) -Peptidase_M27-3qixB02 B: 3-410                                                                                                                                                                                                                                                                                                                                                                                          --------- Pfam domains (2)
         Sec.struct. author .................eeeee...-.....eeeeeee..eeeeeee......---..........--..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeee..-------------.ee.hhhhhhhhhhhhhhhhhh........ee..-----------.eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhhh.hhhhhhhhhh........---..eee...................hhhhh.........hhhhheee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qix B   2 GFVNKQFNYKDPVNGVDIAYIKIPN-GQMQPVKAFKIHNKIWVIPERDTFTNP---DLNPPPEAKQ--VSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEE-------------KFATDPAVTLAHELIHAGHRLYGIAINPNRVFKV-----------EVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYL---KAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNF 419
                                    11        21    | | 31        41        51  |   | 61     |  71        81        91       101       111       121       131       141       151       161       171       181       191      |  -         -|      221       231       241   |     -     | 261       271       281       291       301       311       321       331       341       351       361     | 371       381       391       401       411        
                                                   26 |                        54  58       67 70                                                                                                                             198           212                              245         257                                                                                                           367 371                                                
                                                     28

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Clostridium neurotoxins, catalytic domain (65)

Protein domain: automated matches (23)

Clostridium botulinum [TaxId: 441771] (4)

1a	d3qixa_	A:
1b	d3qixb_	B:

(no "CATH Domain" information available for 3QIX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M27 (28)

Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A) (4)

1a	Peptidase_M27-3qixB01	B:3-410
1b	Peptidase_M27-3qixB02	B:3-410

Asymmetric Unit(hide GO term definitions)

Chain A,B (BXA1_CLOBH | A5HZZ9)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051609	inhibition of neurotransmitter uptake	Any process that prevents the activation of the directed movement of a neurotransmitter into a cell.
	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.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044164	host cell cytosol	The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0044156	host cell junction	A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0044231	host cell presynaptic membrane	A specialized area of membrane of the host axon terminal that faces the plasma membrane of the host neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many host synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
	GO:0044221	host cell synapse	The junction between a nerve fiber of one host neuron and another host neuron or muscle fiber or glial cell; the site of interneuronal communication.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	3qix
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	3.4.24.69
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Description

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Ligands, Modified Residues, Ions (2, 3)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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