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(-) Description

Title :  GAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL)
 
Authors :  L. Joshua-Tor, H. E. Xu, S. A. Johnston, D. C. Rees
Date :  18 Jul 95  (Deposition) - 15 Oct 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Dna-Binding, Peptidase, Cysteine Protease, Regulatory Factor, Bleomycin Hydrolase, Ring Protein, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Joshua-Tor, H. E. Xu, S. A. Johnston, D. C. Rees
Crystal Structure Of A Conserved Protease That Binds Dna: The Bleomycin Hydrolase, Gal6.
Science V. 269 945 1995
PubMed-ID: 7638617
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAL6 HG (EMTS) DERIVATIVE
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: SC277

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HG4Ligand/IonMERCURY (II) ION
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2HG-1Ligand/IonMERCURY (II) ION
3SO418Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:66 , GLY A:395 , LYS A:396 , HOH A:675 , HOH A:714BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREILE A:126 , ARG A:192 , LYS A:196 , TYR A:362 , HOH A:643 , HOH A:644BINDING SITE FOR RESIDUE SO4 A 802
3AC3SOFTWARELYS A:175 , SER A:178 , PRO A:328 , LYS A:329 , HOH A:691 , HOH A:697 , HOH A:698BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWAREPHE A:411 , CYS A:415BINDING SITE FOR RESIDUE HG A 901
5AC5SOFTWARETHR A:55 , CYS A:376 , VAL A:378 , HG A:903BINDING SITE FOR RESIDUE HG A 902
6AC6SOFTWAREVAL A:312 , CYS A:376 , PRO A:385 , HG A:902BINDING SITE FOR RESIDUE HG A 903
7AC7SOFTWAREGLY A:71 , CYS A:73 , ALA A:453BINDING SITE FOR RESIDUE HG A 904
8AC8SOFTWAREGLN A:81 , LEU A:82 , ASN A:85 , LYS A:262 , ARG A:314 , LYS A:319 , ASP A:421 , HOH A:684BINDING SITE FOR RESIDUE GOL A 851
9CATUNKNOWNCYS A:73 , HIS A:369 , ASN A:392NULL

(-) SS Bonds  (0, 0)

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

(-) 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 1GCB)

(-) 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 1GCB)

(-) 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:452
 aligned with BLH1_YEAST | Q01532 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:452
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480  
           BLH1_YEAST    31 SSSIDISKINSWNKEFQSDLTHQLATTVLKNYNADDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRCWLFAATNQLRLNVLSELNLKEFELSQAYLFFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQYSMFLNLVKKYGLIPKDLYGDLPYSTTASRKWNSLLTTKLREFAETLRTALKERSADDSIIVTLREQMQREIFRLMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIKSTPLEFASKYAKLDPSTPVSLINDPRHPYGKLIKIDRLGNVLGGDAVIYLNVDNETLSKLVVKRLQNNKAVFFGSHTPKFMDKKTGVMDIELWNYPAIGYNLPQQKASRIRYHESLMTHAMLITGCHVDETSKLPLRYRVENSWGKDSGKDGLYVMTQKYFEEYCFQIVVDINELPKELASKFTSGKEEPIVLPIWDPMGALA 482
               SCOP domains d1gcba_ A: Bleomycin hydrolase                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------1gcbA01 A:54-453 Cysteine proteinases                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.hhhhhhhhhh....hhhhh..hhhhhhh......eee...............hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh........hhhhhhhhhhh....hhh.....hhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..........eeeeeee.....eeeeeeehhhhhhh........eeeee.........eeee............eeee..hhhhhhhhhhhhh....eeeee....eeee..eeee.....hhhh.......hhhhhh.......eeeeeeeee.........eeeee...........eeeeehhhhhhheeeeeeehhh..hhhhhhhh......eee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcb A   2 SSSIDISKINSWNKEFQSDLTHQLATTVLKNYNADDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRCWLFAATNQLRLNVLSELNLKEFELSQAYLFFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQYSMFLNLVKKYGLIPKDLYGDLPYSTTASRKWNSLLTTKLREFAETLRTALKERSADDSIIVTLREQMQREIFRLMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIKSTPLEFASKYAKLDPSTPVSLINDPRHPYGKLIKIDRLGNVLGGDAVIYLNVDNETLSKLVVKRLQNNKAVFFGSHTPKFMDKKTGVMDIELWNYPAIGYNLPQQKASRIRYHESLMTHAMLITGCHVDETSKLPLRYRVENSWGKDSGKDGLYVMTQKYFEEYCFQIVVDINELPKELASKFTSGKEEPIVLPIWDPMGALA 453
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451
   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 1GCB)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLH1_YEAST | Q01532: 1a6r 2dzy 2dzz 2e00 2e01 2e02 2e03 3gcb

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