4IZJ - JenaLib

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Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YELLOWTAIL ASCITES VIRUS VP4 PROTEASE WITH A WILD-TYPE ACTIVE SITE REVEALS ACYL-ENZYME COMPLEXES AND PRODUCT COMPLEXES.

Authors :   M. Paetzel, I. Y. W. Chung

Date :   30 Jan 13 (Deposition) - 27 Feb 13 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

Keywords :   Viral Protease, Birnavirus, Serine-Lysine Dyad Mechanism, Alpha-Beta Protein Fold, Lysine General Base, Acyl-Enzyme, Product Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Y. Chung, M. Paetzel
Crystal Structures Of Yellowtail Ascites Virus Vp4 Protease Trapping An Internal Cleavage Site Trans Acyl-Enzyme Comple In A Native Ser/Lys Dyad Active Site.
J. Biol. Chem. V. 288 13068 2013
PubMed-ID: 23511637 | Reference-DOI: 10.1074/JBC.M112.386953

Molecule 1 - YELLOWTAIL ASCITES VIRUS (YAV) VP4 PROTEASE
	Chains	:	A, E
	EC Number	:	3.4.21.115
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B+
	Expression System Strain	:	TUNER (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VIRAL PROTEIN 4 (VP4)
	Mutation	:	YES
	Organism Scientific	:	YELLOWTAIL ASCITES VIRUS
	Organism Taxid	:	360000
	Strain	:	Y-6

Molecule 2 - YELLOWTAIL ASCITES VIRUS (YAV) VP4 PROTEASE
	Chains	:	B, C
	EC Number	:	3.4.21.115
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B+
	Expression System Strain	:	TUNER (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VIRAL PROTEIN 4 (VP4)
	Mutation	:	YES
	Organism Scientific	:	YELLOWTAIL ASCITES VIRUS
	Organism Taxid	:	360000
	Strain	:	Y-6

Molecule 3 - YELLOWTAIL ASCITES VIRUS (YAV) VP4 PROTEASE
	Chains	:	D
	EC Number	:	3.4.21.115
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B+
	Expression System Strain	:	TUNER (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VIRAL PROTEIN 4 (VP4)
	Mutation	:	YES
	Organism Scientific	:	YELLOWTAIL ASCITES VIRUS
	Organism Taxid	:	360000
	Strain	:	Y-6

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 15)

No.	Name	Count	Type	Full Name
1	BME	6	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	7	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 5 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:534 , PRO A:535	BINDING SITE FOR RESIDUE BME A 801
2	AC2	SOFTWARE	ASP A:602 , HOH A:907 , HOH A:940	BINDING SITE FOR RESIDUE MG A 802
3	AC3	SOFTWARE	ASP B:644 , THR B:699 , SER B:700 , HOH B:957	BINDING SITE FOR RESIDUE BME B 801
4	AC4	SOFTWARE	ILE B:645 , LYS B:647 , VAL B:649 , PRO B:650	BINDING SITE FOR RESIDUE BME B 802
5	AC5	SOFTWARE	LEU C:524 , ASN C:528 , HIS C:547 , PHE C:557 , VAL C:624 , HOH C:914	BINDING SITE FOR RESIDUE BME C 801
6	AC6	SOFTWARE	ARG D:523 , SER D:551 , GLN E:707	BINDING SITE FOR RESIDUE GOL D 801
7	AC7	SOFTWARE	PRO D:574 , GLN D:577	BINDING SITE FOR RESIDUE BME D 802

Asymmetric Unit

No.	Residues
1	A:588	-	A:604
2	B:588	-	B:604
3	C:588	-	C:604
4	D:588	-	D:604
5	E:588	-	E:604

(no "Cis Peptide Bond" information available for 4IZJ)

(no "SAP(SNP)/Variant" information available for 4IZJ)

(no "PROSITE Motif" information available for 4IZJ)

(no "Exon" information available for 4IZJ)

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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeee......eeeeeeee......eeeeeeeeeee..hhhhhhhhhh.eee......eee.............eeeeeeeeee.....eeeee..........hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhh....eee......ee..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izj A 514 GRFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKDGNIVVEKVFAGPAMGPScQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPIcGVDIKAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   523       533       543       553       563       573       583       593       603       613       623       633|      643       653       663     | 673       683       693       703       713   
                                                                                                                                                  634-CSO                            669-CSO

Chain B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeee......eeeeeeee........eeeeeeeee..hhhhhhhhhh.eee.hhh.eeee............eeeeeeeeeee.....eeeee.....ee...hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhhh...eee......ee..hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izj B 515 RFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKDGNIVVEKVFAGPAMGPScQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPICGVDIKAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
                                                                                                                                                 634-CSO

Chain C from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeee......eeeeeeee......eeeeeeeeeee..hhhhhhhhhh.eee.hhhh.eee.............eeeeeeeeee.....eeeee.....ee...hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhh....eee......ee..hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izj C 514 GRFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKDGNIVVEKVFAGPAMGPScQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPICGVDIKAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   523       533       543       553       563       573       583       593       603       613       623       633|      643       653       663       673       683       693       703       713   
                                                                                                                                                  634-CSO

Chain D from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeee......eeeeeeee......eeeeeeeeeee..hhhhhhhhhh.eee.hhhh.eee.............eeeeeeeeee.....eeeee.....ee...hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhhh...eee......ee..hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izj D 514 GRFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKDGNIVVEKVFAGPAMGPSCQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPIcGVDIKAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663     | 673       683       693       703       713   
                                                                                                                                                                                     669-CSO

Chain E from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeee......eeeeeee.......eeeeeeeeeee..hhhhhhhhhh.eee......eee.............eeeeeeeeee.....eeeee..........hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhhh...eee......ee..hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izj E 514 GRFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKDGNIVVEKVFAGPAMGPScQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPIcGVDIKAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   523       533       543       553       563       573       583       593       603       613       623       633|      643       653       663     | 673       683       693       703       713   
                                                                                                                                                  634-CSO                            669-CSO

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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2gef	CRYSTAL STRUCTURE OF VP4 PROTEASE FROM BLOTCHED SNAKEHEAD VIRUS (BSNV)
2pnl	CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P1
2pnm	CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P6122
3p06	CRYSTAL STRUCTURE OF VP4 PROTEASE FROM TELLINA VIRUS 1 (TV- 1)
4izk

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (7, 7)

SS Bonds (5, 5)

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