1SH3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (MGSO4 CRYSTAL FORM)

Authors :   K. K. Ng, N. Pendas-Franco, J. Rojo, J. A. Boga, A. Machin, J. M. Alonso, F

Date :   24 Feb 04 (Deposition) - 09 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Rna Polymerase, Viral Replication Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. K. Ng, N. Pendas-Franco, J. Rojo, J. A. Boga, A. Machin, J. M. Alonso, F. Parra
Crystal Structure Of Norwalk Virus Polymerase Reveals The Carboxyl Terminus In The Active Site Cleft.
J. Biol. Chem. V. 279 16638 2004
PubMed-ID: 14764591 | Reference-DOI: 10.1074/JBC.M400584200

Molecule 1 - RNA POLYMERASE
	Chains	:	A, B
	EC Number	:	2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	XL-1 BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINUS
	Organism Scientific	:	NORWALK VIRUS
	Organism Taxid	:	11983

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:240 , ASP A:344 , THR A:389	BINDING SITE FOR RESIDUE MG A 600
2	AC2	SOFTWARE	ASP B:240 , ASP B:344 , GLU B:345 , THR B:389	BINDING SITE FOR RESIDUE MG B 600

(no "SS Bond" information available for 1SH3)

Asymmetric Unit

No.	Residues
1	His A:121	-	Pro A:122
2	His B:121	-	Pro B:122

(no "SAP(SNP)/Variant" information available for 1SH3)

(no "PROSITE Motif" information available for 1SH3)

(no "Exon" information available for 1SH3)

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:502
 aligned with Q70ET3_9CALI | Q70ET3 from UniProtKB/TrEMBL  Length:838

    Alignment length:502
                                   343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833  
         Q70ET3_9CALI   334 GTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNED 835
               SCOP domains d1sh3a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1sh3A03 A:216-251,A:301-387         -------------------------------------------------1sh3A03 A:216-251,A:301-387  [code=3.30.70.270, no name defined]                       1sh3A04 A:388-507  [code=1.20.960.20, no name defined]                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeee..........eeeee...........ee..............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhh.............hhhhhh......hhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeee....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh.......................ee..eeeeee..eeeeeehhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sh3 A   6 GTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNED 507
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505

Chain B from PDB  Type:PROTEIN  Length:503
 aligned with Q70ET3_9CALI | Q70ET3 from UniProtKB/TrEMBL  Length:838

    Alignment length:503
                                   342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832   
         Q70ET3_9CALI   333 KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNED 835
               SCOP domains d1sh3b_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1sh3B03 B:216-251,B:301-387         -------------------------------------------------1sh3B03 B:216-251,B:301-387  [code=3.30.70.270, no name defined]                       1sh3B04 B:388-507  [code=1.20.960.20, no name defined]                                                                   CATH domains
           Pfam domains (1) ---------------RdRP_1-1sh3B01 B:20-492                                                                                                                                                                                                                                                                                                                                                                                                                                                                  --------------- Pfam domains (1)
           Pfam domains (2) ---------------RdRP_1-1sh3B02 B:20-492                                                                                                                                                                                                                                                                                                                                                                                                                                                                  --------------- Pfam domains (2)
         Sec.struct. author ........eeee.........eeeee...........ee..............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh......hhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee...........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhh......................ee..eeeeee..eeeeeehhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sh3 B   5 KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNED 507
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504

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: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: RNA-dependent RNA-polymerase (253)

Protein domain: Viral RNA polymerase (148)

Norwalk virus [TaxId: 11983] (7)

1a	d1sh3a_	A:
1b	d1sh3b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.270, no name defined] (278)

Norwalk virus. Organism_taxid: 11983. (3)

1a	1sh3A03	A:216-251,A:301-387
1b	1sh3B03	B:216-251,B:301-387

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Mitochondrial Import Receptor Subunit Tom20; Chain A (25)

Homologous Superfamily: [code=1.20.960.20, no name defined] (24)

Norwalk virus. Organism_taxid: 11983. (3)

2a	1sh3A04	A:388-507
2b	1sh3B04	B:388-507

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RdRP (210)

Family: RdRP_1 (44)

Norwalk virus (3)

1a	RdRP_1-1sh3B01	B:20-492
1b	RdRP_1-1sh3B02	B:20-492

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q70ET3_9CALI | Q70ET3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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: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: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: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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		His A:121 - Pro A:122	[ RasMol ]
		His B:121 - Pro B:122	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1sh3
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	2.7.7.48
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UniProtKB/TrEMBL
	Q70ET3_9CALI \| Q70ET3	:	1sh0 1sh2 3bsn 3bso 3h5x 3h5y 4qpx 5tsn

1khv	RHDV RNA POLYMERASE
1sh0	CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (TRICLINIC)
1sh2	CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (METAL-FREE, CENTERED ORTHORHOMBIC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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CATH Domains (2, 4)

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Gene Ontology (13, 13)

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