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(-) Description

Title :  INHIBITION OF PROTEINASE K BY METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE. AN X-RAY STUDY AT 2.2-ANGSTROMS RESOLUTION
 
Authors :  W. M. Wolf, J. Bajorath, A. Mueller, S. Raghunathan, T. P. Singh, W. Hinr W. Saenger
Date :  07 Aug 91  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Serine Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. M. Wolf, J. Bajorath, A. Muller, S. Raghunathan, T. P. Singh, W. Hinrichs, W. Saenger
Inhibition Of Proteinase K By Methoxysuccinyl-Ala-Ala-Pro-Ala-Chloromethyl Ketone. An X-Ray Study At 2. 2-A Resolution.
J. Biol. Chem. V. 266 17695 1991
PubMed-ID: 1894649
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEINASE K
    Chains: E
    EC Number: 3.4.21.64
    Engineered: YES
    Gene: PROK
    Organism Scientific: ENGYODONTIUM ALBUM
    Organism Taxid: 37998
    Tissue: LIMBER
 
Molecule 2 - METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE
    Chains: I
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
2ALV1Mod. Amino Acid(2S)-2-AMINOPROPANE-1,1-DIOL
3CA1Ligand/IonCALCIUM ION
4MSU1Mod. Amino AcidSUCCINIC ACID MONOMETHYL ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO E:175 , VAL E:177 , ASP E:200 , HOH E:293 , HOH E:294 , HOH E:295 , HOH E:296BINDING SITE FOR RESIDUE CA E 500
2AC2SOFTWAREHIS E:69 , LEU E:96 , GLY E:100 , GLY E:102 , TYR E:104 , SER E:132 , LEU E:133 , GLY E:134 , ASN E:161 , THR E:223 , SER E:224 , HOH I:453 , HOH I:455BINDING SITE FOR CHAIN I OF METHOXYSUCCINYL-ALA- ALA-PRO-ALA-CHLOROMETHYL KETONE

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1E:34 -E:123
2E:178 -E:249

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser E:170 -Pro E:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.PRTK_PARAQ140-151  1E:35-46
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.PRTK_PARAQ174-184  1E:69-79
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.PRTK_PARAQ327-337  1E:222-232

(-) Exons   (0, 0)

(no "Exon" information available for 3PRK)

(-) 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 E from PDB  Type:PROTEIN  Length:279
 aligned with PRTK_PARAQ | P06873 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:279
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         
           PRTK_PARAQ   106 AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA 384
               SCOP domains d3prke_ E: Proteinase K                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3prkE00 E:1-279  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeehhhhhhhhh.....eeeee.......eeeeeeee...........eeeeeeee........hhhhhhhhhhhh.........eeeeeeee......hhhhhhhhhhhhhhhhhhh....eeeeee..eeeehhhhhhhhhhhhhhhheeeeee........eee.......eeeeeee...............eeeeeeeeeeeee...eeeee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhheee..........eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SUBTILASE_AS----------------------SUBTILASE_H----------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S----------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prk E   1 AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         


Chain I from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3prk I 280 xAAPxx 285
                            |   ||
                          280-MSU|
                              284-ALV
                               285-0QE
   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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (PRTK_PARAQ | P06873)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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  PRTK_PARAQ | P06873
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  3.4.21.64
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRTK_PARAQ | P06873: 1bjr 1cnm 1egq 1ht3 1ic6 1oyo 1p7v 1p7w 1pek 1pfg 1pj8 1ptk 2dp4 2dqk 2duj 2g4v 2hd4 2hpz 2id8 2pkc 2pq2 2prk 2pwa 2pwb 2pyz 2v8b 3aj8 3aj9 3d9q 3ddz 3de0 3de1 3de2 3de3 3de4 3de5 3de6 3de7 3dvq 3dvr 3dvs 3dw1 3dw3 3dwe 3dyb 3gt3 3gt4 3i2y 3i30 3i34 3i37 3l1k 3osz 3ptl 3q40 3q5g 3qmp 4b5l 4dj5 4fon 4wob 4woc 4zar 5amx 5avj 5avk 5b1d 5b1e 5cw1 5i9s 5k7s 5kxu 5kxv 5uvl

(-) Related Entries Specified in the PDB File

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