2A97 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE F

Authors :   R. Agarwal, T. Binz, S. Swaminathan

Date :   11 Jul 05 (Deposition) - 20 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Clostridium Botulinum Neurotoxin Serotype F; Light Chain; Catalytic Domain; X-Ray; Crystal Structure; Zinc Endopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Agarwal, T. Binz, S. Swaminathan
Structural Analysis Of Botulinum Neurotoxin Serotype F Light Chain: Implications On Substrate Binding And Inhibitor Design
Biochemistry V. 44 11758 2005
PubMed-ID: 16128577 | Reference-DOI: 10.1021/BI0510072
(for further references see the PDB file header)

Molecule 1 - BOTULINUM NEUROTOXIN TYPE F
	Chains	:	A, B
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	T7
	Fragment	:	CATALYTIC DOMAIN, LIGHT CHAIN
	Gene	:	BOTF
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	1491
	Strain	:	NCTC 10821
	Synonym	:	BONT/F; BONTOXILYSIN F; SEROTYPE F LIGHT CHAIN

		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, 9)

No.	Name	Count	Type	Full Name
1	CD	7	Ligand/Ion	CADMIUM ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:227 , HIS A:231 , GLU A:266 , HOH A:5595	BINDING SITE FOR RESIDUE ZN A 1437
02	AC2	SOFTWARE	HIS B:227 , HIS B:231 , GLU B:266 , HOH B:5596	BINDING SITE FOR RESIDUE ZN B 2437
03	AC3	SOFTWARE	ASP A:383 , HOH A:5510 , ASP B:383 , HOH B:5621	BINDING SITE FOR RESIDUE CD A 5500
04	AC4	SOFTWARE	ASP A:121 , HOH A:5574 , HOH A:5596 , HOH B:5583	BINDING SITE FOR RESIDUE CD A 5502
05	AC5	SOFTWARE	HOH B:5550 , HOH B:5582 , HOH B:5602	BINDING SITE FOR RESIDUE CD B 5503
06	AC6	SOFTWARE	GLU A:127	BINDING SITE FOR RESIDUE CD A 5504
07	AC7	SOFTWARE	ASP B:121 , HOH B:5622 , HOH B:5623 , HOH B:5624 , HOH B:5632	BINDING SITE FOR RESIDUE CD B 5505
08	AC8	SOFTWARE	GLU A:246 , HIS B:122 , HOH B:5506 , HOH B:5584	BINDING SITE FOR RESIDUE CD A 5506
09	AC9	SOFTWARE	HIS A:122 , GLU B:246 , HOH B:5611 , HOH B:5620	BINDING SITE FOR RESIDUE CD A 5507
10	CDA	AUTHOR	HOH B:5582 , HOH B:5550 , HOH B:5602	FIRST CADMIUM BINDING SITE
11	CDB	AUTHOR	ASP B:121 , HOH B:5588 , HOH B:5584 , HOH B:5509	SECOND CADMIUM BINDING SITE
12	CDD	AUTHOR	ASP A:121	FOURT CADMIUM BINDING SITE
13	CDE	AUTHOR	ASP A:383	FIFTH CADMIUM BINDING SITE
14	CDF	AUTHOR	HIS A:122	SIXTH CADMIUM BINDING SITE
15	ZNA	AUTHOR	HIS A:227 , HIS A:231 , GLU A:266 , HOH A:5595	FIRST ZINC BINDING SITE
16	ZNB	AUTHOR	HIS B:227 , HIS B:231 , GLU B:266 , HOH B:5596	SECOND ZINC BINDING SITE

(no "SS Bond" information available for 2A97)

(no "Cis Peptide Bond" information available for 2A97)

(no "SAP(SNP)/Variant" information available for 2A97)

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.	BXF_CLOBO	224-233	2	A:224-233 B:224-233

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.	BXF_CLOBO	224-233	1	A:224-233 -

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.	BXF_CLOBO	224-233	1	- B:224-233

(no "Exon" information available for 2A97)

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:392
 aligned with BXF_CLOBO | P30996 from UniProtKB/Swiss-Prot  Length:1274

    Alignment length:414
                                    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    
            BXF_CLOBO     2 PVAINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTNPSDFDPPASLKNGSSAYYDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGKVLLQEISYAKPYLGNDHTPIDEFSPVTRTTSVNIKLSTNVESSMLLNLLVLGAGPDIFESCCYPVRKLIDPDVVYDPSNYGFGSINIVTFSPEYEYTFNDISGGHNSSTESFIADPAISLAHELIHALHGLYGARGVTYEETIEVKQAPLMIAEKPIRLEEFLTFGGQDLNIITSAMKEKIYNNLLANYEKIATRLSEVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIYKKLYSFTESDLANKFKVKCRNTYFIKYEFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQSIKLNPKIIDS 415
               SCOP domains d2a97a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2a97A00 A:2-415 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeee....hhhhh..eeeeeee..eeeeeee.....hhhhhh...................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....................eeeee.....eeeee..eeeee........eeee..ee.....eehhhhh.....eeee....eeeee.----------..ee.hhhhhhhhhhhhhhhhhh...........------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhh..hhhhhhhhhh............eee.................hhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a97 A   2 PVAINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTNPSDFDPPASLKNGSSAYYDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGKVLLQEISYAKPYLGNDHTPIDEFSPVTRTTSVNIKLSTNVESSMLLNLLVLGAGPDIFESCCYPVRKLIDPDVVYDPSNYGFGSINIVTFSPEYEYTFN----------ESFIADPAISLAHELIHALHGLYGARGVTYEETI------------PIRLEEFLTFGGQDLNIITSAMKEKIYNNLLANYEKIATRLSEVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIYKKLYSFTESDLANKFKVKCRNTYFIKYEFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQSIKLNPKIIDS 415
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  |      -   |   221       231       241      |  -       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
                                                                                                                                                                                                                                    204        215                              248          261

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with BXF_CLOBO | P30996 from UniProtKB/Swiss-Prot  Length:1274

    Alignment length:414
                                    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    
            BXF_CLOBO     2 PVAINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTNPSDFDPPASLKNGSSAYYDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGKVLLQEISYAKPYLGNDHTPIDEFSPVTRTTSVNIKLSTNVESSMLLNLLVLGAGPDIFESCCYPVRKLIDPDVVYDPSNYGFGSINIVTFSPEYEYTFNDISGGHNSSTESFIADPAISLAHELIHALHGLYGARGVTYEETIEVKQAPLMIAEKPIRLEEFLTFGGQDLNIITSAMKEKIYNNLLANYEKIATRLSEVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIYKKLYSFTESDLANKFKVKCRNTYFIKYEFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQSIKLNPKIIDS 415
               SCOP domains d2a97b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2a97B00 B:2-415 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeee...........eeeeeee..eeeeeee.....hhhhhh...................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......................eeeee.....eeeee..eeeee........eeee..ee.....ee..........eeee....ee.ee.----------..ee.hhhhhhhhhhhhhhhhhh...........------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhh..hhhhhhhhh..............ee.................hhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a97 B   2 PVAINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTNPSDFDPPASLKNGSSAYYDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGKVLLQEISYAKPYLGNDHTPIDEFSPVTRTTSVNIKLSTNVESSMLLNLLVLGAGPDIFESCCYPVRKLIDPDVVYDPSNYGFGSINIVTFSPEYEYTFN----------ESFIADPAISLAHELIHALHGLYGARGVTYEETI------------PIRLEEFLTFGGQDLNIITSAMKEKIYNNLLANYEKIATRLSEVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIYKKLYSFTESDLANKFKVKCRNTYFIKYEFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQSIKLNPKIIDS 415
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  |      -   |   221       231       241      |  -       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
                                                                                                                                                                                                                                    204        215                              248          261

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: 1491] (19)

1a	d2a97a_	A:
1b	d2a97b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Zincin-like (46)

Homologous Superfamily: Metalloproteases ('zincins'), catalytic domain like (46)

Clostridium botulinum. Organism_taxid: 1491. Strain: nctc 10821. (2)

1a	2a97A00	A:2-415
1b	2a97B00	B:2-415

(no "Pfam Domain" information available for 2A97)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BXF_CLOBO | P30996)

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:0008320	protein transmembrane transporter activity	Enables the transfer of a protein from one side of a membrane to the other.
	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:0071806	protein transmembrane transport	The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
	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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2a8a	CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE F LIGHT CHAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (16, 16)

SS Bonds (0, 0)

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