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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION
 
Authors :  W. J. Mcgrath, J. Ding, R. M. Sweet, W. F. Mangel
Date :  07 Jan 03  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiol Hydrolase, Viral Proteinase, Peptide Cofactor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Mcgrath, J. Ding, A. Didwania, R. M. Sweet, W. F. Mangel
Crystallographic Structure At 1. 6-A Resolution Of The Human Adenovirus Proteinase In A Covalent Complex With Its 11-Amino-Acid Peptide Cofactor: Insights On A New Fold
Biochim. Biophys. Acta V. 1648 1 2003
PubMed-ID: 12758141  |  Reference-DOI: 10.1016/S1570-9639(03)00024-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENAIN
    Chains: A
    EC Number: 3.4.22.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET13
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ADENOVIRUS PROTEINASE
    Gene: L3-23K
    Organism Scientific: HUMAN ADENOVIRUS 2
    Organism Taxid: 10515
    Synonym: ENDOPROTEASE, LATE L3 23 KDA PROTEIN
 
Molecule 2 - PVIC
    Chains: B
    Engineered: YES
    Fragment: PVIC PEPTIDE
    Other Details: CHEMICALLY SYNTHESIZED C-TERMINAL 11 AMINO ACIDS FROM HUMAN ADENOVIRUS SEROTYPE 2 PVI MOLECULE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:146 , MET A:157 , GLN A:162 , ARG A:180 , HIS A:181 , HOH A:1017BINDING SITE FOR RESIDUE ACY A 600

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:104 -B:309

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NLN)

(-) 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:203
 aligned with PRO_ADE02 | P03252 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
            PRO_ADE02     2 GSSEQELKAIVKDLGCGPYFLGTYDKRFPGFVSPHKLACAIVNTAGRETGGVHWMAFAWNPRSKTCYLFEPFGFSDQRLKQVYQFEYESLLRRSAIASSPDRCITLEKSTQSVQGPNSAACGLFCCMFLHAFANWPQTPMDHNPTMNLITGVPNSMLNSPQVQPTLRRNQEQLYSFLERHSPYFRSHSAQIRSATSFCHLKNM 204
               SCOP domains d1nlna_ A: Human adenovirus 2 proteinase, adenain                                                                                                                                                           SCOP domains
               CATH domains 1nlnA00 A:2-204 Adenoviral Proteinase; Chain A                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhh.eeeee.............eeeeee..........eeeeeee....eeeee.....hhhhhhhhhh..hhhhhhhhhhhhh...eeeeeee.ee.......hhhhhhhhhhhhhhhh.........hhhhh..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nln A   2 GSSEQELKAIVKDLGCGPYFLGTYDKRFPGFVSPHKLACAIVNTAGRETGGVHWMAFAWNPRSKTCYLFEPFGFSDQRLKQVYQFEYESLLRRSAIASSPDRCITLEKSTQSVQGPNSAACGLFCCMFLHAFANWPQTPMDHNPTMNLITGVPNSMLNSPQVQPTLRRNQEQLYSFLERHSPYFRSHSAQIRSATSFCHLKNM 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with CAP6_ADE02 | P03274 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:11
                                   249 
           CAP6_ADE02   240 GVQSLKRRRCF 250
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1nln B 300 GVQSLKRRRCF 310
                                   309
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRO_ADE02 | P03252)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain B   (CAP6_ADE02 | P03274)
biological process
    GO:0039664    lysis of host organelle involved in viral entry into host cell    The viral-induced lysis of an organelle (endosome, lysosome, or caveosome) that is involved in the uptake of a virus into a host cell. Occurs once the virus is within the organelle, and results in transfer of the viral contents from the organelle compartment into the cytoplasm.
    GO:0075521    microtubule-dependent intracellular transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
    GO:0039708    nuclear capsid assembly    The assembly of a virus capsid that occurs in the nucleus. The assembly of large icosahedral shells for herpesviridae and adenoviridae requires structural proteins that act as chaperones for assembly.
    GO:0075606    transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CAP6_ADE02 | P03274: 1avp 4pid 4pie 5fgy
        PRO_ADE02 | P03252: 1avp 4ekf 4pid 4pie 5fgy

(-) Related Entries Specified in the PDB File

1avp THE SAME COMPLEX AT HIGH RESOLUTION