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(-) Description

Title :  STRUCTURE OF KUMAMOLISIN-AS COMPLEXED WITH A COVALENTLY-BOUND INHIBITOR, ACIPF
 
Authors :  M. Li, A. Wlodawer, A. Gustchina, N. Tsuruoka, M. Ashida, H. Minakata, H K. Oda, T. Nishino, T. Nakayama
Date :  01 Mar 04  (Deposition) - 30 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Kumamolisin-As, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wlodawer, M. Li, A. Gustchina, N. Tsuruoka, M. Ashida, H. Minakata, H. Oyama, K. Oda, T. Nishino, T. Nakayama
Crystallographic And Biochemical Investigations Of Kumamolisin-As, A Serine-Carboxyl Peptidase With Collagenas Activity
J. Biol. Chem. V. 279 21500 2004
PubMed-ID: 15014068  |  Reference-DOI: 10.1074/JBC.M401141200

(-) Compounds

Molecule 1 - KUMAMOLISIN-AS
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ALICYCLOBACILLUS SENDAIENSIS
    Organism Taxid: 192387
 
Molecule 2 - ACE-ILE-PRO-PHL PEPTIDE INHIBITOR
    Chains: D, E, F
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2CA3Ligand/IonCALCIUM ION
3PHL3Mod. Amino AcidL-PHENYLALANINOL
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA-1Ligand/IonCALCIUM ION
3PHL1Mod. Amino AcidL-PHENYLALANINOL
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA-1Ligand/IonCALCIUM ION
3PHL1Mod. Amino AcidL-PHENYLALANINOL
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA-1Ligand/IonCALCIUM ION
3PHL1Mod. Amino AcidL-PHENYLALANINOL
4SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , GLY A:20 , ARG A:290 , HOH A:1583 , HOH A:1808 , HOH A:1853 , HOH A:2353BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREASP A:316 , ILE A:317 , GLY A:334 , GLY A:336 , ASP A:338 , HOH A:1501BINDING SITE FOR RESIDUE CA A 601
3AC3SOFTWAREGLU B:133 , ASP B:134 , TYR B:176 , HIS B:177 , VAL B:178 , ARG B:223 , HOH B:1721 , HOH B:2056 , HOH B:2196BINDING SITE FOR RESIDUE SO4 B 502
4AC4SOFTWAREASP B:316 , ILE B:317 , GLY B:334 , GLY B:336 , ASP B:338 , HOH B:2501BINDING SITE FOR RESIDUE CA B 602
5AC5SOFTWARELYS C:121 , ARG C:327 , GLN C:329 , HOH C:1862 , HOH C:1995 , HOH C:2120BINDING SITE FOR RESIDUE SO4 C 503
6AC6SOFTWAREASP C:316 , ILE C:317 , GLY C:334 , GLY C:336 , ASP C:338 , HOH C:3501BINDING SITE FOR RESIDUE CA C 603
7AC7SOFTWAREGLU A:78 , ASN A:102 , SER A:128 , TRP A:129 , GLY A:130 , ASP A:164 , ASP A:179 , GLY A:276 , THR A:277 , SER A:278 , HOH D:1824 , HOH D:1972 , HOH D:2402BINDING SITE FOR CHAIN D OF ACE-ILE-PRO-PHL PEPTIDE INHIBITOR
8AC8SOFTWAREGLU B:78 , ASN B:102 , SER B:128 , TRP B:129 , GLY B:130 , ASP B:164 , ASP B:179 , GLY B:276 , THR B:277 , SER B:278 , HOH B:1751 , HOH E:1940BINDING SITE FOR CHAIN E OF ACE-ILE-PRO-PHL PEPTIDE INHIBITOR
9AC9SOFTWAREGLU C:78 , ASN C:102 , SER C:128 , TRP C:129 , GLY C:130 , ASP C:164 , ASP C:179 , GLY C:276 , THR C:277 , SER C:278 , HOH F:2377 , HOH F:2385BINDING SITE FOR CHAIN F OF ACE-ILE-PRO-PHL PEPTIDE INHIBITOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Phe A:180 -Pro A:181
2Val A:250 -Pro A:251
3Ile A:330 -Tyr A:331
4Phe B:180 -Pro B:181
5Val B:250 -Pro B:251
6Ile B:330 -Tyr B:331
7Phe C:180 -Pro C:181
8Val C:250 -Pro C:251
9Ile C:330 -Tyr C:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SIO)

(-) Sequences/Alignments

Asymmetric 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 Q8GB88_9BACL | Q8GB88 from UniProtKB/TrEMBL  Length:553

    Alignment length:357
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       
         Q8GB88_9BACL   190 AAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLP 546
               SCOP domains d1sioa_ A: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1sioA00 A:1-357  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhh...........eeeeee.....hhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh.......eeee.eeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhh.........ee.......eeeeeeeeeee..eeeeeee............ee......hhhhh................ee..eeee.hhhheeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sio A   1 AAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLP 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       


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with Q8GB88_9BACL | Q8GB88 from UniProtKB/TrEMBL  Length:553

    Alignment length:356
                                   200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540      
         Q8GB88_9BACL   191 APTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLP 546
               SCOP domains d1siob_ B: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1sioB00 B:2-357  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhh...........eeeeee.....hhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh......eeee.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.................ee.......eeeeeeeeeee..eeeeeee..hhhhhh....ee......hhhhh................ee..eeee....eeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sio B   2 APTAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLP 357
                                    11        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      


Chain C from PDB  Type:PROTEIN  Length:353
 aligned with Q8GB88_9BACL | Q8GB88 from UniProtKB/TrEMBL  Length:553

    Alignment length:353
                                   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   
         Q8GB88_9BACL   193 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALL 545
               SCOP domains d1sioc_ C: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1sioC00 C:4-356  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------------------------------------------------------------------------Peptidase_S8-1sioC01 C:77-337                                                                                                                                                                                                                                        ------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------Peptidase_S8-1sioC02 C:77-337                                                                                                                                                                                                                                        ------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------Peptidase_S8-1sioC03 C:77-337                                                                                                                                                                                                                                        ------------------- Pfam domains (3)
         Sec.struct. author .eehhhhhhhhh...........eeeeee.....hhhhhhhhhhhh......eeeee.............hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh......eeee.eeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhh.........ee.......eeeeeeeeeee..eeeeeee..hhhhhh....ee......hhhhh................ee..eeee.hhhheeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sio C   4 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALL 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1sio D   1 xIPf   4
                            |  |
                            1-ACE
                               4-PHL


Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1sio E   1 xIPf   4
                            |  |
                            |  |
                            1-ACE
                               4-PHL


Chain F from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1sio F   1 xIPf   4
                            |  |
                            |  |
                            1-ACE
                               4-PHL
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8GB88_9BACL | Q8GB88)
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
        Q8GB88_9BACL | Q8GB88: 1siu 1sn7 1zvj 1zvk 4ne7

(-) Related Entries Specified in the PDB File

1siu KUMAMOLISIN-AS E78H MUTANT