1Q31 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TOBACCO ETCH VIRUS PROTEASE C151A MUTANT

Authors :   C. M. Nunn, S. Djordjevic, R. R. George, G. T. Urquhart, L. H. Chao, Y. Tsu

Date :   28 Jul 03 (Deposition) - 02 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   3C-Type Protease, Tev, Two-Domain, Antiparallel, Beta-Barrel, Trypsin-Like, C151A, Viral Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Nunn, M. Jeeves, M. J. Cliff, G. T. Urquhart, R. R. George, L. H. Chao, Y. Tscuchia, S. Djordjevic
Crystal Structure Of Tobacco Etch Virus Protease Shows The Protein C Terminus Bound Within The Active Site.
J. Mol. Biol. V. 350 145 2005
PubMed-ID: 15919091 | Reference-DOI: 10.1016/J.JMB.2005.04.013

Molecule 1 - NUCLEAR INCLUSION PROTEIN A
	Chains	:	A, B
	EC Number	:	3.4.22.44
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRET3ATEV
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	TOBACCO ETCH VIRUS
	Organism Taxid	:	12227
	Synonym	:	TOBACCO ETCH VIRUS PROTEASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:130	BINDING SITE FOR RESIDUE BME B 901
2	AC2	SOFTWARE	CYS A:130 , TRP A:143	BINDING SITE FOR RESIDUE BME A 902

(no "SS Bond" information available for 1Q31)

(no "Cis Peptide Bond" information available for 1Q31)

(no "SAP(SNP)/Variant" information available for 1Q31)

(no "PROSITE Motif" information available for 1Q31)

(no "Exon" information available for 1Q31)

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:227
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:239
                                  2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270         
            POLG_TEV   2041 LFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKPEEPFQPVKEATQLMNELVYSQ 2279
               SCOP domains d1q31a_ A: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                                                      SCOP domains
               CATH domains ----1q31A01   1q31A02 A:18-98,A:182-206 Trypsin-like serine proteases                          1q31A01 A:8-17,A:99-181,A:207-221 Trypsin-like serine proteases                    1q31A02 A:18-98,A:182-2061q31A01        --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhheeeeeeee...eeeeeeeee..eeee.hhhhh...eeeeeee..eeeee.hhhh.eeee......eeee.....................eeeeeeee......eeee...ee........eeee...........eeee.....eeeeeeee......eeeee...hhhhhhhh......ee.......eeee..eeee.....------------....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q31 A    4 LFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQAGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKPE------------MNELVYSQ  242
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        |-         - |       
                                                                                                                                                                                                                                                    222          235

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:239
                                  2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270         
            POLG_TEV   2041 LFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKPEEPFQPVKEATQLMNELVYSQ 2279
               SCOP domains d1q31b_ B: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                                                      SCOP domains
               CATH domains ----1q31B01   1q31B02 B:18-98,B:182-206 Trypsin-like serine proteases                          1q31B01 B:8-17,B:99-181,B:207-221 Trypsin-like serine proteases                    1q31B02 B:18-98,B:182-2061q31B01        --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhheeeeeeee...eeeeeeeee..eeeee.hhhh...eeeeeee..eeeee.hhhh.eeee.....eeeee.....................eeeeee....hhhhh.ee...ee........eeee...........eeee.....eeeeeeee......eeeee...hhhhhhhh......ee.......eeee..eeee....-------------....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q31 B    4 LFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQAGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKP-------------MNELVYSQ  242
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       | -         - |       
                                                                                                                                                                                                                                                   221           235

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( (-)

)

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	d1q31a_	A:
1b	d1q31b_	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	1q31A01	A:8-17,A:99-181,A:207-221
1b	1q31B01	B:8-17,B:99-181,B:207-221
1c	1q31A02	A:18-98,A:182-206
1d	1q31B02	B:18-98,B:182-206

(no "Pfam Domain" information available for 1Q31)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	3.4.22.44
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	POLG_TEV \| P04517	:	1lvb 1lvm

1lvb	C151A MUTANT OF TEV PROTEASE COMPLEXED WITH A SUBSTRATE
1lvm	S219D MUTANT OF TEV PROTEASE COMPLEXED WITH PRODUCT

Description

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