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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN SEROTYPE A WITH INHIBITORY PEPTIDE RRGI

Authors :   D. Kumaran, S. Swaminathan

Date :   11 Feb 08 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.47

Chains :   Asym./Biol. Unit : A,B

Keywords :   Botulinum Neurotoxin Type A, Catalytic Domain, Endopeptidase, Bio- Warfare Agent, Metalloprotease, Protease, Secreted, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kumaran, R. Rawat, M. L. Ludivico, S. A. Ahmed, S. Swaminathan
Structure- And Substrate-Based Inhibitor Design For Clostridium Botulinum Neurotoxin Serotype A
J. Biol. Chem. V. 283 18883 2008
PubMed-ID: 18434312 | Reference-DOI: 10.1074/JBC.M801240200

Molecule 1 - BOTULINUM NEUROTOXIN A LIGHT CHAIN
	Atcc	:	3502
	Chains	:	A
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21-DE3 RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-424
	Gene	:	BOTA
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	1491
	Strain	:	HALL
	Synonym	:	BONTOXILYSIN-A

Molecule 2 - INHIBITOR PEPTIDE RRGI
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP
2	SO4	3	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:223 , HIS A:227 , GLU A:262 , ARG B:500	BINDING SITE FOR RESIDUE ZN A 450
2	AC2	SOFTWARE	LYS A:340 , HOH A:584	BINDING SITE FOR RESIDUE SO4 A 451
3	AC3	SOFTWARE	ASN A:174 , LEU A:175 , THR A:176 , ASN A:394 , HOH A:484 , HOH A:598 , HOH A:675	BINDING SITE FOR RESIDUE SO4 A 452
4	AC4	SOFTWARE	ARG A:231 , HOH A:514 , HOH A:552 , HOH A:788 , ARG B:500	BINDING SITE FOR RESIDUE SO4 A 453
5	AC5	SOFTWARE	VAL A:70 , ILE A:161 , PHE A:163 , GLU A:164 , PHE A:194 , HIS A:223 , GLU A:224 , HIS A:227 , TYR A:251 , LEU A:256 , GLU A:262 , ARG A:363 , TYR A:366 , ASN A:368 , PHE A:369 , ASP A:370 , PHE A:423 , ZN A:450 , SO4 A:453 , HOH A:471 , HOH A:537 , HOH A:637 , HOH A:823 , HOH B:105	BINDING SITE FOR CHAIN B OF INHIBITOR PEPTIDE RRGI

(no "SS Bond" information available for 3C8B)

(no "Cis Peptide Bond" information available for 3C8B)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_BXA1_CLOBO_001 *	V	27	A	BXA1_CLOBO	---	---	A	A	27	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (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
1	ZINC_PROTEASE	PS00142		BXA1_CLOBO	220-229	1	A:220-229

(no "Exon" information available for 3C8B)

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
	(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:423
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:423
                                    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       380       390       400       410       420   
           BXA1_CLOBH     1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
               SCOP domains d3c8ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.........eeeeeee..eeeeeee....hhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeee..hhhhhh........ee.hhhhhhhhhhhhhhhhhh........eee...hhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhhh.hhhhhhhhhh............eeee.................................hhhhheeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8b A   1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
                                    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       380       390       400       410       420

Chain A from PDB  Type:PROTEIN  Length:423
 aligned with BXA1_CLOBO | P10845 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:423
                                    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       380       390       400       410       420   
           BXA1_CLOBO     1 MPFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
               SCOP domains d3c8ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.........eeeeeee..eeeeeee....hhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eee.................eeee....eeeee..hhhhhh........ee.hhhhhhhhhhhhhhhhhh........eee...hhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhhh.hhhhhhhhhh............eeee.................................hhhhheeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8b A   1 MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLF 423
                                    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       380       390       400       410       420

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3c8b B 500 RRGIx 504
                                |
                              504-NH2

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/Biological 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: 1491] (19)

d3c8ba_

(no "CATH Domain" information available for 3C8B)

(no "Pfam Domain" information available for 3C8B)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BXA1_CLOBO | P10845)

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: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).
	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.

Chain A (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c8b)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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