1LVM - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT

Authors :   J. Phan, A. Zdanov, A. G. Evdokimov, J. E. Tropea, H. K. Peters Iii, R. B. Kapust, M. Li, A. Wlodawer, D. S. Waugh

Date :   28 May 02 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,C,E  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A,B,C,D,E  (1x)

Keywords :   Beta Barrel, Chymotrypsin-Type Cystein Protease, Enzyme- Peptide Complex, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Phan, A. Zdanov, A. G. Evdokimov, J. E. Tropea, H. K. Peters Iii, R. B. Kapust, M. Li, A. Wlodawer, D. S. Waugh
Structural Basis For The Substrate Specificity Of Tobacco Etch Virus Protease.
J. Biol. Chem. V. 277 50564 2002
PubMed-ID: 12377789 | Reference-DOI: 10.1074/JBC.M207224200
(for further references see the PDB file header)

Molecule 1 - CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21(DE3)
	Expression System Strain	:	PRK529
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-221
	Mutation	:	YES
	Organism Scientific	:	TOBACCO ETCH VIRUS
	Organism Taxid	:	12227

Molecule 2 - OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21(DE3)
	Expression System Strain	:	PRK529
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 302-310
	Organism Scientific	:	TOBACCO ETCH VIRUS
	Organism Taxid	:	12227

Molecule 3 - CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21(DE3)
	Expression System Strain	:	PRK529
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 230-236
	Organism Scientific	:	TOBACCO ETCH VIRUS
	Organism Taxid	:	12227

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A		C		E
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:214 , HOH C:81	BINDING SITE FOR RESIDUE ACE C 301
2	AC2	SOFTWARE	HOH D:133 , HOH D:176 , HOH D:421	BINDING SITE FOR RESIDUE ACE D 301

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTYVIRUS_NIA_PRO	PS51436	Potyvirus NIa protease (NIa-pro) domain profile.	POLG_TEV	2038-2255	1	A:1-218

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTYVIRUS_NIA_PRO	PS51436	Potyvirus NIa protease (NIa-pro) domain profile.	POLG_TEV	2038-2255	1	A:1-218

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTYVIRUS_NIA_PRO	PS51436	Potyvirus NIa protease (NIa-pro) domain profile.	POLG_TEV	2038-2255	0	-

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTYVIRUS_NIA_PRO	PS51436	Potyvirus NIa protease (NIa-pro) domain profile.	POLG_TEV	2038-2255	1	A:1-218

(no "Exon" information available for 1LVM)

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:229
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:229
                                  2039      2049      2059      2069      2079      2089      2099      2109      2119      2129      2139      2149      2159      2169      2179      2189      2199      2209      2219      2229      2239      2249         
            POLG_TEV   2030 KNEDLTFEGESLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKP 2258
               SCOP domains d1lvm.1 A:,E: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                                         SCOP domains
               CATH domains ---------------1lvmA01   1lvmA02 A:18-98,A:182-206 Trypsin-like serine proteases                          1lvmA01 A:8-17,A:99-181,A:207-221 Trypsin-like serine proteases                    1lvmA02 A:18-98,A:182-2061lvmA01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhh.eeeeeeee..eeeeeeeeee..eeeehhhhhhh...eeeeee..eeeee.hhhh.eeee......eeee.....................eeeeeeee......eeee...ee.eee....eeee...........eeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhh.eee.......eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------POTYVIRUS_NIA_PRO  PDB: A:1-218 UniProt: 2038-2255                                                                                                                                                                        --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvm A   -8 GHHHHHHHGESLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMDKP  221
                                   ||2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
                                  -1|                                                                                                                                                                                                                            
                                    1

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:219
                                  2049      2059      2069      2079      2089      2099      2109      2119      2129      2139      2149      2159      2169      2179      2189      2199      2209      2219      2229      2239      2249         
            POLG_TEV   2040 SLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKP 2258
               SCOP domains d1lvmb_ B: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                                  SCOP domains
               CATH domains -----1lvmB01   1lvmB02 B:18-98,B:182-206 Trypsin-like serine proteases                          1lvmB01 B:8-17,B:99-181,B:207-221 Trypsin-like serine proteases                    1lvmB02 B:18-98,B:182-2061lvmB01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.eeeeeeee..eeeeeeeeee..eeeehhhhhh...eeeeeee..eeeee.hhhh.eeee......eeee.....................eeeeeee...hhhh.eee...ee.eee....eeee...........eeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhh.eee.......eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE POTYVIRUS_NIA_PRO  PDB: - UniProt: 2038-2255                                                                                                                                                                            --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvm B    3 SLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMDKP  221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:7
            POLG_TEV   2785 TENLYFQ 2791
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                1lvm C  301 xENLYFQ  307
                            |      
                          301-ACE

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:7
            POLG_TEV   2785 TENLYFQ 2791
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                1lvm D  301 xENLYFQ  307
                            |      
                            |      
                          301-ACE

Chain E from PDB  Type:PROTEIN  Length:7
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:7
            POLG_TEV   2267 EATQLMN 2273
               SCOP domains d1lvm.1 SCOP domains
               CATH domains ------- CATH domains
           Pfam domains (1) Pep---- Pfam domains (1)
           Pfam domains (2) Pep---- Pfam domains (2)
           Pfam domains (3) Pep---- Pfam domains (3)
         Sec.struct. author ..ee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                1lvm E  230 EATQLMN  236

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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Viral proteases (62)

Protein domain: TEV protease (nucleat inclusion protein A, NIA) (3)

Tobacco etch virus, TEV [TaxId: 12227] (3)

1a	d1lvm.1	A:,E:
1b	d1lvmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Tobacco etch virus. Organism_taxid: 12227. (3)

1a	1lvmA01	A:8-17,A:99-181,A:207-221
1b	1lvmB01	B:8-17,B:99-181,B:207-221
1c	1lvmA02	A:18-98,A:182-206
1d	1lvmB02	B:18-98,B:182-206

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Peptidase_C4 (3)

Tobacco etch virus (TEV) (2)

1a	Peptidase_C4-1lvmE01	E:230-232
1b	Peptidase_C4-1lvmE02	E:230-232
1c	Peptidase_C4-1lvmE03	E:230-232

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (POLG_TEV | P04517)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0018144	RNA-protein covalent cross-linking	The formation of a covalent cross-link between RNA and a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
	GO:0019029	helical viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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	POLG_TEV \| P04517	:	1lvb 1q31

1lvb	CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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