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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF MUTANT W129A OF KUMAMOLISIN, A SEDOLISIN TYPE PROTEINASE (PREVIOUSLY CALLED KUMAMOLYSIN OR KSCP)
 
Authors :  M. Comellas-Bigler, K. Maskos, R. Huber, H. Oyama, K. Oda, W. Bode
Date :  16 Apr 04  (Deposition) - 03 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine-Carboxyl Proteinases, Subtilases, Catalytic Mechanism, Sedolisin, Kumamolisin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Comellas-Bigler, K. Maskos, R. Huber, H. Oyama, K. Oda, W. Bode
1. 2 A Crystal Structure Of The Serine Carboxyl Proteinase Pro-Kumamolisin: Structure Of An Intact Pro-Subtilase
Structure V. 12 1313 2004
PubMed-ID: 15242607  |  Reference-DOI: 10.1016/J.STR.2004.04.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KUMAMOLISIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM 109
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Gene: KSCP
    Mutation: YES
    Organism Scientific: BACILLUS SP. MN-32
    Organism Taxid: 198803

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:316 , ILE A:317 , GLY A:334 , GLY A:336 , ASP A:338 , HOH A:368BINDING SITE FOR RESIDUE CA A 365
2AC2SOFTWAREASN A:145 , ARG A:146 , LEU A:149 , TYR A:186 , SER A:198 , ALA A:199 , PHE A:225 , PRO A:226 , HOH A:384 , HOH A:404 , HOH A:407 , HOH A:412 , HOH A:431 , HOH A:433 , HOH A:475 , HOH A:491 , HOH A:562 , HOH A:667BINDING SITE FOR RESIDUE SO4 A 366
3AC3SOFTWARELYS A:121 , ARG A:327 , ARG A:329 , HOH A:387 , HOH A:415 , HOH A:466 , HOH A:524 , HOH A:597BINDING SITE FOR RESIDUE SO4 A 367

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T1I)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:180 -Pro A:181
2Val A:250 -Pro A:251
3Ile A:330 -Tyr A:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T1I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T1I)

(-) Exons   (0, 0)

(no "Exon" information available for 1T1I)

(-) 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:357
 aligned with Q8RR56_9BACI | Q8RR56 from UniProtKB/TrEMBL  Length:552

    Alignment length:357
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       
         Q8RR56_9BACI   189 AAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDETSLAQYFASLGVSAPQVVSVSVDGATNQPTGDPNGPDGEVELDIEVAGALAPGAKIAVYFAPNTDAGFLNAITTAVHDPTHKPSIVSISWGGPEDSWAPASIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASAGRIERETVWNDGPDGGSTGGGVSRIFPLPSWQERANVPPSANPGAGSGRGVPDVAGNADPATGYEVVIDGETTVIGGTSAVAPLFAALVARINQKLGKPVGYLNPTLYQLPPEVFHDITEGNNDIANRARIYQAGPGWDPCTGLGSPIGIRLLQALLP 545
               SCOP domains d1t1ia_ A: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t1iA00 A:1-357  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------Peptidase_S8-1t1iA01 A:76-331                                                                                                                                                                                                                                   -------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhh...........eeeeee.....hhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeee..........................eeeeeeeeee....eeeeee..hhhhhh....ee......hhhhh................ee..eeee....eeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t1i A   1 AAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDETSLAQYFASLGVSAPQVVSVSVDGATNQPTGDPNGPDGEVELDIEVAGALAPGAKIAVYFAPNTDAGFLNAITTAVHDPTHKPSIVSISAGGPEDSWAPASIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASAGRIERETVWNDGPDGGSTGGGVSRIFPLPSWQERANVPPSANPGAGSGRGVPDVAGNADPATGYEVVIDGETTVIGGTSAVAPLFAALVARINQKLGKPVGYLNPTLYQLPPEVFHDITEGNNDIANRARIYQAGPGWDPCTGLGSPIGIRLLQALLP 357
                                    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       280       290       300       310       320       330       340       350
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8RR56_9BACI | Q8RR56)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q8RR56_9BACI | Q8RR56: 1gt9 1gtg 1gtj 1gtl 1t1e 1t1g

(-) Related Entries Specified in the PDB File

1gt9 NATIVE KUMAMOLISIN CATALYTIC DOMAIN
1gtg NATIVE KUMAMOLISIN CATALYTIC DOMAIN
1gtj KUMAMOLISIN IN COMPLEX WITH AC-ILE-ALA-PHE-CHO
1gtl KUMAMOLISIN IN COMPLEX WITH AC-ILE-PRO-PHE-CHO
1t1e INTACT PRO-KUMAMOLISIN
1t1g MUTANT E32A OF KUMAMOLYISIN CATALYTIC DOMAIN