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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE INTACT PRO-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 :  1.18
Chains :  Asym./Biol. Unit :  A
Keywords :  Proenzyme, Prosubtilase, Activation Mechanism, Sedolisin, Serine-Carboxyl Proteinase, 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
    Gene: KSCP
    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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:505 , ILE A:506 , GLY A:523 , GLY A:525 , ASP A:527 , HOH A:701BINDING SITE FOR RESIDUE CA A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T1E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:190 -Pro A:192
2Phe A:369 -Pro A:370
3Val A:439 -Pro A:440

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T1E)

(-) Exons   (0, 0)

(no "Exon" information available for 1T1E)

(-) 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:534
 aligned with Q8RR56_9BACI | Q8RR56 from UniProtKB/TrEMBL  Length:552

    Alignment length:534
                                    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       461       471       481       491       501       511       521       531       541    
         Q8RR56_9BACI    12 EKREVLAGHARRQAPQAVDKGPVTGDQRISVTVVLRRQRGDELEAHVERQAALAPHARVHLEREAFAASHGASLDDFAEIRKFAEAHGLTLDRAHVAAGTAVLSGPVDAVNQAFGVELRHFDHPDGSYRSYVGDVRVPASIAPLIEAVFGLDTRPVARPHFRLRRRAEGEFEARSQSAAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDETSLAQYFASLGVSAPQVVSVSVDGATNQPTGDPNGPDGEVELDIEVAGALAPGAKIAVYFAPNTDAGFLNAITTAVHDPTHKPSIVSISWGGPEDSWAPASIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASAGRIERETVWNDGPDGGSTGGGVSRIFPLPSWQERANVPPSANPGAGSGRGVPDVAGNADPATGYEVVIDGETTVIGGTSAVAPLFAALVARINQKLGKPVGYLNPTLYQLPPEVFHDITEGNNDIANRARIYQAGPGWDPCTGLGSPIGIRLLQALLP 545
               SCOP domains d1t1ea2 A:12-190 Pro-kumamolisin activation domain                                                                                                                                 d1t1ea1 A:192-546 Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------1t1eA02 A:175-546  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------Pro-kuma_activ-1t1eA02 A:26-165                                                                                                             --------------------------------------------------------------------------------------------------Peptidase_S8-1t1eA01 A:265-520                                                                                                                                                                                                                                  -------------------------- Pfam domains
         Sec.struct. author ..eee............eeeee.....eeeeeeee...hhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhh...eeee.....eee.....eee..hhh.eeeee........ee..ee....................hhhhhhhhh...........eeeeee.....hhhhhhhhhhhhh.....eeeee.............hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh.......eeee.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh.........ee.......eeeeeeeeeee..eeeeeee..hhhhhh....ee...........................ee..eeee.hhhhheeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t1e A  12 EKREVLAGHARRQAPQAVDKGPVTGDQRISVTVVLRRQRGDELEAHVERQAALAPHARVHLEREAFAASHGASLDDFAEIRKFAEAHGLTLDRAHVAAGTAVLSGPVDAVNQAFGVELRHFDHPDGSYRSYVGDVRVPASIAPLIEAVLGLDTRPVARPHFRLRRRAEGEFEARSQSAAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDETSLAQYFASLGVSAPQVVSVSVDGATNQPTGDPNGPDGEVELDIEVAGALAPGAKIAVYFAPNTDAGFLNAITTAVHDPTHKPSIVSISWGGPEDSWAPASIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASAGRIERETVWNDGPDGGSTGGGVSRIFPLPSWQERANVPPSANPGAGSGRGVPDVAGNADPATGYEVVIDGETTVIGGTAAVAPLFAALVARINQKLGKPVGYLNPTLYQLPPEVFHDITEGNNDIANRARIYQAGPGWDPCTGLGSPIGIRLLQALLP 546
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542    
                                                                                                                                                                                                            190|                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                             192
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)
(-)
Clan: no clan defined [family: Pro-kuma_activ] (1)

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q8RR56_9BACI | Q8RR56: 1gt9 1gtg 1gtj 1gtl 1t1g 1t1i

(-) Related Entries Specified in the PDB File

1gt9 NATIVE KUMAMOLISIN CATALYTIC DOMAIN
1gtg NATIVE KUMAMOLISIN CATALYTIC DOMAIN
1gtj KUMAMOLISIN CATALYTIC DOMAIN IN COMPLEX WITH AC-ILE-ALA-PHE -CHO
1gtl KUMAMOLISIN CATALYTIC DOMAIN IN COMPLEX WITH AC-ILE-PRO-PHE -CHO
1t1g HIGH RESOLUTION CRYSTAL STRUCTURE OF MUTANT E23A OF KUMAMOLISIN, A SEDOLISIN TYPE PROTEINASE
1t1i HIGH RESOLUTION CRYSTAL STRUCTURE OF MUTANT W129A OF KUMAMOLISIN, A SEDOLISIN TYPE PROTEINASE