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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE ALPHA-LYTIC PROTEASE AT 1.6 A, PH 5.14
 
Authors :  A. I. Derman, T. Mau, D. A. Agard
Date :  16 Jun 99  (Deposition) - 18 Jun 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Folding, Pro Region, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Derman, T. Mau, D. A. Agard
A Genetic Screen That Targets Specifically The Folding Transition State Of Alpha-Lytic Protease
To Be Published 1999
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-LYTIC PROTEASE
    Chains: A
    EC Number: 3.4.21.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PALP12
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Fragment: MATURE PROTEASE DOMAIN, RESIDUES 1-198
    Organism Scientific: LYSOBACTER ENZYMOGENES
    Organism Taxid: 69

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , ARG A:78 , GLN A:190 , TYR A:191 , HOH A:230 , HOH A:231 , HOH A:232 , HOH A:380 , HOH A:381 , HOH A:382 , HOH A:429BINDING SITE FOR RESIDUE SO4 A 202
2AC2SOFTWAREALA A:1 , ASN A:2 , ARG A:183 , PRO A:186 , HOH A:207 , HOH A:273 , HOH A:342 , HOH A:343 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE SO4 A 203
3AC3SOFTWAREHIS A:36 , ARG A:89 , ARG A:140 , GLY A:141 , SER A:143 , GOL A:201 , HOH A:361 , HOH A:362 , HOH A:363BINDING SITE FOR RESIDUE SO4 A 204
4AC4SOFTWAREHIS A:36 , ARG A:89 , TYR A:123 , GLU A:125 , SER A:159 , GLY A:160 , SO4 A:204BINDING SITE FOR RESIDUE GOL A 201

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:17 -A:37
2A:101 -A:111
3A:137 -A:170

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRLA_LYSEN231-236  1A:32-37
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRLA_LYSEN336-347  1A:137-148

(-) Exons   (0, 0)

(no "Exon" information available for 1QRX)

(-) 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:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
           PRLA_LYSEN   200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 397
               SCOP domains d1qrxa_ A: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --1qrxA01 A:3-76,A:184-196 Trypsin-like serine proteases                    1qrxA02 A:77-183 Trypsin-like serine proteases                                                             1qrxA01      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...eeee..eeeee..eeeeeehhhhh....eeee..eeeeeeeeee.....eeeeee....eeeeeeee..eeee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee.....eeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qrx A   1 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRLA_LYSEN | P00778)
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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1qrx
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  PRLA_LYSEN | P00778
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  3.4.21.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRLA_LYSEN | P00778: 1boq 1gba 1gbb 1gbc 1gbd 1gbe 1gbf 1gbh 1gbi 1gbj 1gbk 1gbl 1gbm 1p01 1p02 1p03 1p04 1p05 1p06 1p09 1p10 1p11 1p12 1qq4 1qrw 1ssx 1tal 2alp 2h5c 2h5d 2lpr 2pro 2ull 3lpr 3m7t 3m7u 3pro 3qgj 3urc 3urd 3ure 4pro 5lpr 6lpr 7lpr 8lpr 9lpr

(-) Related Entries Specified in the PDB File

1qq4 THE STRUCTURE OF THE R102H/G134S MUTANT AT THE SAME PH (5.14).
1tal THE TRUCTURE OF SAME MOLECULE DETERMINED AT PH 8. IN ADDITION, THE TRIS MOLECULE (TAM) IN 1TAL SHOULD HAVE BEEN MODELED AS A GLYCEROL MOLECULE, AS IT IS DONE IN THIS ENTRY.