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(-) Description

Title :  CRYSTAL STRUCTURE OF ALKALINE SERINE PROTEASE KP-43 FROM BACILLUS SP. KSM-KP43 (OXIDIZED FORM, 1.73 ANGSTROM)
 
Authors :  T. Nonaka, M. Fujihashi, A. Kita, K. Saeki, S. Ito, K. Horikoshi, K. Miki
Date :  08 Jul 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Hydrolase Fold, Jelly-Roll Beta-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nonaka, M. Fujihashi, A. Kita, K. Saeki, S. Ito, K. Horikoshi, K. Mik
The Crystal Structure Of An Oxidatively Stable Subtilisin-Like Alkaline Serine Protease, Kp-43, With A C-Terminal {Beta}-Barrel Domain
J. Biol. Chem. V. 279 47344 2004
PubMed-ID: 15342641  |  Reference-DOI: 10.1074/JBC.M409089200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A
    EC Number: 3.4.21.-
    Fragment: RESIDUES 1-434
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 109322
    Strain: KSM-KP43
    Synonym: ALKALINE SERINE PROTEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
3GOL1Ligand/IonGLYCEROL
4SME2Mod. Amino AcidMETHIONINE SULFOXIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:186 , SER A:194 , ASP A:197 , HIS A:201 , HOH A:3001 , HOH A:3002BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREASP A:384 , THR A:386 , PRO A:388 , ASP A:391 , ASN A:392 , HOH A:3003BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREASP A:367 , LEU A:368 , ASP A:369 , ASP A:394 , GLU A:400 , HOH A:3004BINDING SITE FOR RESIDUE CA A 1003
4AC4SOFTWARETRP A:130 , GLY A:131 , ALA A:159 , GLY A:161 , THR A:254 , SER A:255BINDING SITE FOR RESIDUE DIO A 2001
5AC5SOFTWAREALA A:133 , ASN A:135 , GLU A:163 , ALA A:319 , TYR A:320 , HOH A:3141 , HOH A:3242BINDING SITE FOR RESIDUE GOL A 2101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:164 -Pro A:165
2Ala A:172 -Pro A:173
3Gly A:209 -Pro A:210
4Lys A:217 -Pro A:218
5Tyr A:300 -Pro A:301
6Ser A:387 -Pro A:388
7Gly A:424 -Pro A:425

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WMF)

(-) 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:434
 aligned with Q93UV9_9BACI | Q93UV9 from UniProtKB/TrEMBL  Length:640

    Alignment length:434
                                   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636    
         Q93UV9_9BACI   207 NDVARGIVKADVAQSSYGLYGQGQIVAVADTGLDTGRNDSSMHEAFRGKITALYALGRTNNANDTNGHGTHVAGSVLGNGSTNKGMAPQANLVFQSIMDSGGGLGGLPSNLQTLFSQAYSAGARIHTNSWGAAVNGAYTTDSRNVDDYVRKNDMTILFAAGNEGPNGGTISAPGTAKNAITVGATENLRPSFGSYADNINHVAQFSSRGPTKDGRIKPDVMAPGTFILSARSSLAPDSSFWANHDSKYAYMGGTSMATPIVAGNVAQLREHFVKNRGITPKPSLLKAALIAGAADIGLGYPNGNQGWGRVTLDKSLNVAYVNESSSLSTSQKATYSFTATAGKPLKISLVWSDAPASTTASVTLVNDLDLVITAPNGTQYVGNDFTSPYNDNWDGRNNVENVFINAPQSGTYTIEVQAYNVPVGPQTFSLAIVN 640
               SCOP domains d1wmfa2 A:1-318 Alkaline serine protease kp-43, N-terminal domain                                                                                                                                                                                                                                                             d1wmfa1 A:319-434 Alkaline serine protease kp-43, C-terminal domain                                                  SCOP domains
               CATH domains 1wmfA01 A:1-317  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                         1wmfA02 A:318-434  [code=2.60.120.380, no name defined]                                                               CATH domains
               Pfam domains ------------------------Peptidase_S8-1wmfA02 A:25-317                                                                                                                                                                                                                                                                        -------------PPC-1wmfA01 A:331-418                                                                   ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh........eeeeee...................eeeeee...........hhhhhhhhhhhh............eeeeee.............hhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhh..eeeee....................eeeeee...hhhhhhhhh......................eeee...eeee.....hhhhh.ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.................hhhhhhh.eeeeeeeee....eeeeeeee.....eeeeee................eeeeeee.....eee.................eeeeee.....eeeeeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmf A   1 NDVARGIVKADVAQSSYGLYGQGQIVAVADTGLDTGRNDSSMHEAFRGKITALYALGRTNNANDTNGHGTHVAGSVLGNGSTNKGMAPQANLVFQSIMDSGGGLGGLPSNLQTLFSQAYSAGARIHTNSWGAAVNGAYTTDSRNVDDYVRKNDMTILFAAGNEGPNGGTISAPGTAKNAITVGATENLRPSFGSYADNINHVAQFSSRGPTKDGRIKPDVMAPGTFILSARSSLAPDSSFWANHDSKYAYmGGTSmATPIVAGNVAQLREHFVKNRGITPKPSLLKAALIAGAADIGLGYPNGNQGWGRVTLDKSLNVAYVNESSSLSTSQKATYSFTATAGKPLKISLVWSDAPASTTASVTLVNDLDLVITAPNGTQYVGNDFTSPYNDNWDGRNNVENVFINAPQSGTYTIEVQAYNVPVGPQTFSLAIVN 434
                                    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       360       370       380       390       400       410       420       430    
                                                                                                                                                                                                                                                                                    251-SME|                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                         256-SME
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q93UV9_9BACI | Q93UV9)
molecular function
    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).
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)

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        Q93UV9_9BACI | Q93UV9: 1wmd 1wme

(-) Related Entries Specified in the PDB File

1wmd THE NATIVE FORM AT 1.30 ANGSTROM
1wme THE NATIVE FORM AT 1.50 ANGSTROM