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(-) Description

Title :  COMPLEX OF SUBSTRATE ADP-RIBOSE WITH IBV NSP3 ADRP DOMAIN
 
Authors :  Y. Xu, L. Cong, C. Chen, L. Wei, Q. Zhao, X. Xu, Y. Ma, M. Bartlam, Z. Rao
Date :  16 Oct 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Globular Like, Cytoplasm, Hydrolase, Membrane, Metal- Binding, Protease, Ribosomal Frameshifting, Rna-Binding, Thiol Protease, Transmembrane, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xu, L. Cong, C. Chen, L. Wei, Q. Zhao, X. Xu, Y. Ma, M. Bartlam, Z. Rao
Crystal Structures Of Two Coronavirus Adp-Ribose-1''-Monophosphatases And Their Complexes With Adp-Ribose: A Systematic Structural Analysis Of The Viral Adrp Domain.
J. Virol. V. 83 1083 2009
PubMed-ID: 18987156  |  Reference-DOI: 10.1128/JVI.01862-08
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 3
    Chains: A, B
    EC Number: 3.4.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NSP3 ADRP DOMAIN
    Gene: 1A
    Organism Common: IBV
    Organism Scientific: AVIAN INFECTIOUS BRONCHITIS VIRUS
    Synonym: NSP3, PAPAIN-LIKE PROTEINASE, PL-PRO, P195

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , LEU A:21 , ALA A:40 , ASN A:42 , GLY A:49 , GLY A:50 , VAL A:51 , ALA A:52 , ALA A:54 , VAL A:128 , SER A:130 , SER A:131 , GLY A:132 , ILE A:133 , PHE A:134 , PHE A:159 , SER A:160 , LEU A:161 , HOH A:183 , HOH A:193 , HOH A:196 , HOH A:201 , HOH A:223 , HOH A:228BINDING SITE FOR RESIDUE APR A 175
2AC2SOFTWARELYS A:139 , GLY B:19 , ASP B:20 , LEU B:21 , ALA B:40 , ASN B:42 , SER B:46 , GLY B:49 , GLY B:50 , VAL B:51 , ALA B:52 , ALA B:54 , ARG B:99 , VAL B:128 , SER B:130 , SER B:131 , GLY B:132 , ILE B:133 , PHE B:134 , PHE B:159 , SER B:160 , LEU B:161 , HOH B:184 , HOH B:202 , HOH B:210BINDING SITE FOR RESIDUE APR B 175

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EWP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EWP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EWP)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.R1A_IBVM1005-1181  1A:1-174
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.R1A_IBVM1005-1181  1A:1-174
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.R1A_IBVM1005-1181  1A:1-174
Biological Unit 3 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACROPS51154 Macro domain profile.R1A_IBVM1005-1181  0-

(-) Exons   (0, 0)

(no "Exon" information available for 3EWP)

(-) Sequences/Alignments

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:177
 aligned with R1A_IBVM | P0C6V5 from UniProtKB/Swiss-Prot  Length:3953

    Alignment length:187
                                  1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171       
            R1A_IBVM    992 VKAQREKKAKKFKVKPATCEKPKFLEYKTCVGDLAVVIAKALDEFKEFCIVNAANEHMSHGGGVAKAIADFCGPDFVEYCADYVKKHGPQQKLVTPSFVKGIQCVNNVVGPRHGDSNLREKLVAAYKSVLVGGVVNYVVPVLSSGIFGVDFKISIDAMREAFKGCAIRVLLFSLSQEHIDYFDATCK 1178
               SCOP domains d3e          wpa_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------............eeeeee.hhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee......eeeeeee........hhhhhhhhhhhh.......eeeee.........hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------MACRO  PDB: A:1-174 UniProt: 1005-1181                                                                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ewp A   -2 LGS----------VKPATCEKPKFLEYKTCVGDLAVVIAKALDEFKEFCIVNAANEHMSHGGGVAKAIADFCGPDFVEYCADYVKKHGPQQKLVTPSFVKGIQCVNNVVGPRHGDSNLREKLVAAYKSVLVGGVVNYVVPVLSSGIFGVDFKISIDAMREAFKGCAIRVLLFSLSQEHIDYFDATCK  174
                              |      -   |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       
                              0          1                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with R1A_IBVM | P0C6V5 from UniProtKB/Swiss-Prot  Length:3953

    Alignment length:168
                                  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170        
            R1A_IBVM   1011 EKPKFLEYKTCVGDLAVVIAKALDEFKEFCIVNAANEHMSHGGGVAKAIADFCGPDFVEYCADYVKKHGPQQKLVTPSFVKGIQCVNNVVGPRHGDSNLREKLVAAYKSVLVGGVVNYVVPVLSSGIFGVDFKISIDAMREAFKGCAIRVLLFSLSQEHIDYFDATCK 1178
               SCOP domains d3ewpb_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee......eeeeeeee.......hhhhhhhhhhhh.......eeeee.........hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE MACRO  PDB: - UniProt: 1005-1181                                                                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ewp B    7 EKPKFLEYKTCVGDLAVVIAKALDEFKEFCIVNAANEHMSHGGGVAKAIADFCGPDFVEYCADYVKKHGPQQKLVTPSFVKGIQCVNNVVGPRHGDSNLREKLVAAYKSVLVGGVVNYVVPVLSSGIFGVDFKISIDAMREAFKGCAIRVLLFSLSQEHIDYFDATCK  174
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EWP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EWP)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (R1A_IBVM | P0C6V5)
molecular function
    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: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:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    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.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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UniProtKB/Swiss-Prot
        R1A_IBVM | P0C6V5: 3ewo 3ld1

(-) Related Entries Specified in the PDB File

3ewo 3ewq 3ewr