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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
 
Authors :  R. Khayat, R. Batra, M. J. Massariol, L. Lagace, L. Tong
Date :  09 Apr 01  (Deposition) - 06 Jun 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coat Protein, Hydrolase, Serine Protease, Catalytic Triad, Viral Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Khayat, R. Batra, M. J. Massariol, L. Lagace, L. Tong
Investigating The Role Of Histidine 157 In The Catalytic Activity Of Human Cytomegalovirus Protease.
Biochemistry V. 40 6344 2001
PubMed-ID: 11371196  |  Reference-DOI: 10.1021/BI010158B

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 3.4.21.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-256
    Gene: UL80
    Mutation: YES
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10360
    Strain: AD169
    Synonym: HCMV PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IEF)

(-) Sites  (0, 0)

(no "Site" information available for 1IEF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IEF)

(-) 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:208
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:248
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248        
           SCAF_HCMVA     9 QAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
               SCOP domains d1iefa_ A: Human cytomegalovirus pr            otease                                                                                                                                                                                                    SCOP domains
               CATH domains 1iefA00 A:9-256 Serine Protease, Hu            man Cytomegalovirus Protease; Chain A                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee............hhhhhhhhh------------..eeee..eeeeeeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeee..------------------..eeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh----------......hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ief A   9 QAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWL------------ALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLASR------------------FKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ----------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    18        28        38    |    -       |58        68        78        88        98       108       118       128       | -         -      |158       168       178       188       198 |       -  |    218       228       238       248        
                                                             43           56                                                                             136                155                                          200        211                                             


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
           SCAF_HCMVA     4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
               SCOP domains d1iefb_ B: Human cytomegalovirus proteas           e                                                                                                                                                                                                          SCOP domains
               CATH domains 1iefB00 B:304-556 Serine Protease, Human            Cytomegalovirus Protease; Chain A                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhh-----------...eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh.eeeee.------------------...eeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh.--.....--......hhhhhhhhhhhhh...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ief B 304 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWL-----------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLAS------------------PFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQR--STAVD--GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 556
                                   313       323       333       343         - |     363       373       383       393       403       413       423       433 |       -         -|      463       473       483       493       | -|   |  513       523       533       543       553   
                                                                 343         355                                                                             435                454                                            501  | 508  |                                             
                                                                                                                                                                                                                                  504    511
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SCAF_HCMVA | P16753)
molecular function
    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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.

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 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ief
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
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  SCAF_HCMVA | P16753
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  3.4.21.97
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 Related Entries

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

UniProtKB/Swiss-Prot
        SCAF_HCMVA | P16753: 1cmv 1id4 1iec 1ied 1ieg 1jq6 1jq7 1lay 1njt 1nju 1nkk 1nkm 1wpo 2wpo

(-) Related Entries Specified in the PDB File

1id4 CRYSTAL STRUCTURE OF THE H157Q MUTANT OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
1iec CRYSTAL STRUCTURE OF THE H157A MUTANT OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
1ied CRYSTAL STRUCTURE OF THE H157E MUTANT OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
1ief CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
1ieg CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A/H157A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE
1wpo STRUCTURE OF HUMAN CYTOMEGALOVIRUS PROTEASE
2wpo CONSERVED MODE OF PEPTIDOMIMETIC INHIBITION AND SUBSTRATE RECOGNITION OF HUMAN CYTOMEGALOVIRUS PROTEASE