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(-) Description

Title :  STRUCTURE OF BACTERIOPHAGE T4 ENDOII E118A MUTANT
 
Authors :  C. E. Andersson, P. Lagerback, K. Carlson
Date :  07 Sep 09  (Deposition) - 02 Mar 10  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Giy-Yig, Nuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Andersson, P. Lagerback, K. Carlson
Structure Of Bacteriophage T4 Endonuclease Ii Mutant E118A, A Tetrameric Giy-Yig Enzyme.
J. Mol. Biol. V. 397 1003 2010
PubMed-ID: 20156453  |  Reference-DOI: 10.1016/J.JMB.2010.01.076

(-) Compounds

Molecule 1 - ENDONUCLEASE II
    Chains: A, B, C, D
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: RESIDUES 9-144
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:37 , TYR A:47 , ARG A:57 , TYR A:61 , LYS A:76 , HOH A:2070BINDING SITE FOR RESIDUE PO4 A1133
2AC2SOFTWAREILE C:131 , HOH C:2097 , HOH C:2098BINDING SITE FOR RESIDUE PEG C1132
3AC3SOFTWARETRP B:129 , HOH B:2104 , ILE C:131BINDING SITE FOR RESIDUE PEG B1132

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WSH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WSH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WSH)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIY_YIGPS50164 GIY-YIG domain profile.END2_BPT432-131
 
 
 		  4A:32-131
B:32-131
C:32-131
D:32-131

(-) Exons   (0, 0)

(no "Exon" information available for 2WSH)

(-) Sequences/Alignments

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:134
 aligned with END2_BPT4 | P07059 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:134
                              1                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128    
            END2_BPT4     - --MKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSMTNELGTMTIATIDLEEPLFIKLFNPPWNIQ 132
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....eeee...................eeeee......eeee....hhhhhhhhhhh..........hhhhhhhhhh....eeeee...eeeeeee..eeeeee..hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------GIY_YIG  PDB: A:32-131 UniProt: 32-131                                                              - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsh A  -2 HHmKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSmTNELGTmTIATIDLEAPLFIKLFNPPWNIQ 132
                             ||      8        18        28        38        48        58        68        78        88        98   |   108|      118       128    
                             ||                                                                                                  102-MSE  |                       
                            -1|                                                                                                         109-MSE                   
                              1-MSE                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with END2_BPT4 | P07059 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:133
                              1                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128   
            END2_BPT4     - --MKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSMTNELGTMTIATIDLEEPLFIKLFNPPWNI 131
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....eeee...................eeeee......eeee....hhhhhhhhhhh.....--...hhhhhhhhhh....eeeee...eeeeeee..eeeeee..hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------GIY_YIG  PDB: B:32-131 UniProt: 32-131                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsh B  -2 HHmKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDK--DSTKSALIHSALKEGSKVEFYARQCFNLSmTNELGTmTIATIDLEAPLFIKLFNPPWNI 131
                             ||      8        18        28        38        48        58        68 |  |   78        88        98   |   108|      118       128   
                            -1|                                                                   70 73                          102-MSE  |                      
                              1-MSE                                                                                                     109-MSE                  


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with END2_BPT4 | P07059 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:134
                               1                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127    
            END2_BPT4     - ---MKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSMTNELGTMTIATIDLEEPLFIKLFNPPWNI 131
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...............................................hhhhhhhhhhh..-----...hhhhhhhhhh............eeeeeee..eeeeee..hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------GIY_YIG  PDB: C:32-131 UniProt: 32-131                                                               PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsh C  -3 HHHmKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINR-----DSTKSALIHSALKEGSKVEFYARQCFNLSmTNELGTmTIATIDLEAPLFIKLFNPPWNI 131
                              ||     7        17        27        37        47        57        67     |  77        87        97    |  107 |     117       127    
                             -1|                                                                67    73                          102-MSE  |                      
                               1-MSE                                                                                                     109-MSE                  


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with END2_BPT4 | P07059 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:133
                              1                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128   
            END2_BPT4     - --MKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSMTNELGTMTIATIDLEEPLFIKLFNPPWNI 131
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...............................................hhhhhhhhhhh..........hhhhhhhhhh............eeeeeee..eeeeee..hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------GIY_YIG  PDB: D:32-131 UniProt: 32-131                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsh D  -2 HHmKEIATEYSFIKYTELELDDNGSIKQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSmTNELGTmTIATIDLEAPLFIKLFNPPWNI 131
                             ||      8        18        28        38        48        58        68        78        88        98   |   108|      118       128   
                            -1|                                                                                                  102-MSE  |                      
                              1-MSE                                                                                                     109-MSE
   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2WSH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WSH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WSH)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (END2_BPT4 | P07059)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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  2wsh
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