Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454
 
Authors :  L. Joshua-Tor, W. Zheng, S. A. Johnston
Date :  27 Feb 98  (Deposition) - 21 Oct 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Bleomycin Hydrolase, Peptidase, Protease, Dna-Binding Protein, Self- Compartmentalizing Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zheng, S. A. Johnston, L. Joshua-Tor
The Unusual Active Site Of Gal6/Bleomycin Hydrolase Can Act As A Carboxypeptidase, Aminopeptidase, And Peptide Ligase.
Cell(Cambridge, Mass. ) V. 93 103 1998
PubMed-ID: 9546396  |  Reference-DOI: 10.1016/S0092-8674(00)81150-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAL6
    Cell Line: BL21
    Chains: A
    EC Number: 3.4.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: GAL6C73ADELK
    Expression System Plasmid: PKM260/PLYSS
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: GAL6C73ADELK
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: YBH, YEAST BLEOMYCIN HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 42)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2SO430Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1A73UNKNOWNALA A:73NUCLEOPHILIC CYSTEINE MUTATED TO ALANINE.
2AC1SOFTWAREASN A:66 , GLY A:395 , LYS A:396 , HOH A:812 , HOH A:857 , HOH A:907BINDING SITE FOR RESIDUE SO4 A 1101
3AC2SOFTWAREILE A:126 , ARG A:192 , TYR A:362 , HOH A:566 , HOH A:632BINDING SITE FOR RESIDUE SO4 A 1102
4AC3SOFTWAREASN A:273 , TYR A:279 , ASP A:303 , ASN A:304 , HOH A:550 , HOH A:639BINDING SITE FOR RESIDUE SO4 A 1103
5AC4SOFTWARELYS A:175 , SER A:178 , LYS A:329 , HOH A:543BINDING SITE FOR RESIDUE SO4 A 1104
6AC5SOFTWAREARG A:44 , GLU A:341 , HOH A:677 , HOH A:678BINDING SITE FOR RESIDUE SO4 A 1105
7AC6SOFTWAREGLN A:81 , LEU A:82 , ASN A:85 , LYS A:262 , ARG A:314 , LYS A:319 , ASP A:421 , HOH A:595 , HOH A:753BINDING SITE FOR RESIDUE GOL A 1001
8AC7SOFTWAREARG A:129 , GLN A:132 , TYR A:133 , TRP A:446 , HOH A:780 , HOH A:783BINDING SITE FOR RESIDUE GOL A 1002
9NULUNKNOWNHIS A:369 , ASN A:392CATALYTIC RESIDUES.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:62 -Pro A:63
2Thr A:327 -Pro A:328

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.BLH1_YEAST96-107  1A:67-78
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.BLH1_YEAST396-406  1A:367-377
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.BLH1_YEAST96-107  6A:67-78
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.BLH1_YEAST396-406  6A:367-377

(-) Exons   (0, 0)

(no "Exon" information available for 3GCB)

(-) 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:458
 aligned with BLH1_YEAST | Q01532 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:469
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473         
           BLH1_YEAST    14 TFRSHLLRAPQIVLKRMSSSIDISKINSWNKEFQSDLTHQLATTVLKNYNADDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRCWLFAATNQLRLNVLSELNLKEFELSQAYLFFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQYSMFLNLVKKYGLIPKDLYGDLPYSTTASRKWNSLLTTKLREFAETLRTALKERSADDSIIVTLREQMQREIFRLMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIKSTPLEFASKYAKLDPSTPVSLINDPRHPYGKLIKIDRLGNVLGGDAVIYLNVDNETLSKLVVKRLQNNKAVFFGSHTPKFMDKKTGVMDIELWNYPAIGYNLPQQKASRIRYHESLMTHAMLITGCHVDETSKLPLRYRVENSWGKDSGKDGLYVMTQKYFEEYCFQIVVDINELPKELASKFTSGKEEPIVLPIWDPMGALA 482
               SCOP domains d3gc           ba_ A: Bleomycin hydrolase                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------3gcbA01 A:54-453 Cysteine proteinases                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh-----------hhh....hhhhhhhhhhhhh.hhhhhhhhhh....hhhhh..hhhhhhh........................hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........hhhhhhhhhhh....hhh.....hhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..........eeeeeee.....eeeeeeehhhhhhh........eeeee.........eeee...........eeeee..hhhhhhhhhhhhh....eeeee...................hhhh.......hhhhhh.......eeeeeeeee.........eeeee...........eeeeehhhhhhheeeeeeehhh..hhhhhhhh......eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gcb A  -4 AFQG-----------AMASSIDISKINSWNKEFQSDLTHQLATTVLKNYNADDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRAWLFAATNQLRLNVLSELNLKEFELSQAYLFFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQYSMFLNLVKKYGLIPKDLYGDLPYSTTASRKWNSLLTTKLREFAETLRTALKERSADDSIIVTLREQMQREIFRLMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIKSTPLEFASKYAKLDPSTPVSLINDPRHPYGKLIKIDRLGNVLGGDAVIYLNVDNETLSKLVVKRLQNNKAVFFGSHTPKFMDKKTGVMDIELWNYPAIGYNLPQQKASRIRYHESLMTHAMLITGCHVDETSKLPLRYRVENSWGKDSGKDGLYVMTQKYFEEYCFQIVVDINELPKELASKFTSGKEEPIVLPIWDPMGALA 453
                               |     -     |   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
                              -1           0
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (BLH1_YEAST | Q01532)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    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:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0043418    homocysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    A73  [ RasMol ]  +environment [ RasMol ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    NUL  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:327 - Pro A:328   [ RasMol ]  
    Thr A:62 - Pro A:63   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3gcb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BLH1_YEAST | Q01532
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  BLH1_YEAST | Q01532
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BLH1_YEAST | Q01532: 1a6r 1gcb 2dzy 2dzz 2e00 2e01 2e02 2e03

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GCB)