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(-) Description

Title :  THERMOLYSIN COMPLEXED WITH Z-L-ASPARTIC ACID (BENZYLOXYCARBONYL-L-ASPARTIC ACID)
 
Authors :  M. Senda, T. Senda, S. Kidokoro
Date :  10 Dec 01  (Deposition) - 10 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metalloproteinase, Benzyloxycarbonyl Amino Acid, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Senda, T. Senda, S. Kidokoro
Crystal Structure Analyses Of Thermolysin In Complex With Its Inhibitors.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THERMOLYSIN
    Chains: A
    EC Number: 3.4.24.27
    Organism Scientific: BACILLUS THERMOPROTEOLYTICUS
    Organism Taxid: 1427

 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
1ASP1Mod. Amino AcidASPARTIC ACID
2CA4Ligand/IonCALCIUM ION
3PHQ1Ligand/IonBENZYL CHLOROCARBONATE
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:138 , GLU A:177 , ASP A:185 , GLU A:187 , GLU A:190 , HOH A:1320BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:177 , ASN A:183 , ASP A:185 , GLU A:190 , HOH A:1334 , HOH A:1345BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREASP A:57 , ASP A:59 , GLN A:61 , HOH A:1329 , HOH A:1331 , HOH A:1336BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWARETYR A:193 , THR A:194 , ILE A:197 , ASP A:200 , HOH A:1324 , HOH A:1366BINDING SITE FOR RESIDUE CA A 404
5AC5SOFTWAREHIS A:142 , HIS A:146 , GLU A:166 , ASP A:1317BINDING SITE FOR RESIDUE ZN A 405
6AC6SOFTWAREASN A:112 , ALA A:113 , LEU A:133 , VAL A:139 , HIS A:142 , GLU A:143 , ILE A:188 , LEU A:202 , ASP A:1317 , HOH A:1418BINDING SITE FOR RESIDUE PHQ A 317
7AC7SOFTWAREASN A:112 , ALA A:113 , HIS A:142 , GLU A:143 , HIS A:146 , TYR A:157 , GLU A:166 , HIS A:231 , PHQ A:317 , ZN A:405 , HOH A:1498BINDING SITE FOR RESIDUE ASP A 1317

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:50 -Pro A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.THER_BACTH371-380  1A:139-148

(-) Exons   (0, 0)

(no "Exon" information available for 1KKK)

(-) 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:317
 aligned with THER_BACTH | P00800 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:317
                                                                                                                                                                                                                                                                                                                                                     548 
                                   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     | 
          THER_BACTH    233 ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVK-    -
               SCOP domains d1kkka_ A: Thermolysin                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -----1kkkA01 A:6-154  [code=3.10.170.10, no name defined]                                                                                                 1kkkA02 A:155-315 Neutral Protease Domain 2                                                                                                                      -- CATH domains
               Pfam domains ---Peptidase_M4-1kkkA01 A:4-151                                                                                                                        -Peptidase_M4_C-1kkkA02 A:153-315                                                                                                                                   -- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeee...ee.ee......eeeee.........ee.ee...ee.hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee........eee....eee.........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....ee..............ee..hhhhhh...hhhhh...hhhhhhh..hhhhhhhhhhhhhhheee..eee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kkk A    1 ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVKD 1317
                                    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     ||
                                                                                                                                                                                                                                                                                                                                                     316|
                                                                                                                                                                                                                                                                                                                                                     1317
   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) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THER_BACTH | P00800)
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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THER_BACTH | P00800: 1fj3 1fjo 1fjq 1fjt 1fju 1fjv 1fjw 1gxw 1hyt 1kei 1kjo 1kjp 1kl6 1kr6 1kro 1ks7 1kto 1l3f 1lna 1lnb 1lnc 1lnd 1lne 1lnf 1os0 1pe5 1pe7 1pe8 1qf0 1qf1 1qf2 1thl 1tli 1tlp 1tlx 1tmn 1trl 1y3g 1z9g 1zdp 2a7g 2g4z 2tli 2tlx 2tmn 2whz 2wi0 3dnz 3do0 3do1 3do2 3eim 3f28 3f2p 3fb0 3fbo 3fcq 3fgd 3flf 3for 3fv4 3fvp 3fxp 3fxs 3ls7 3ms3 3msa 3msf 3msn 3n21 3nn7 3p7p 3p7q 3p7r 3p7s 3p7t 3p7u 3p7v 3p7w 3qgo 3qh1 3qh5 3ssb 3t2h 3t2i 3t2j 3t73 3t74 3t87 3t8c 3t8d 3t8f 3t8g 3t8h 3tli 3tmn 3zi6 4d91 4d9w 4h57 4mtw 4mwp 4mxj 4mzn 4n4e 4n5p 4n66 4oi5 4ow3 4tli 4tln 4tmn 4tnl 5a3y 5dpe 5dpf 5fsj 5fsp 5fss 5fxn 5js3 5jss 5jt9 5jvi 5jxn 5k7t 5l3u 5l41 5l8p 5lif 5lwd 5mnr 5n2t 5n2x 5n2z 5n31 5n34 5n3v 5n3y 5tli 5tln 5tmn 5un3 5uu7 5uu8 5uu9 5uua 5uub 5uuc 5uud 5uue 6tli 6tmn 7tli 7tln 8tli 8tln

(-) Related Entries Specified in the PDB File

1kei 1KEI CONTAINS THE SAME PROTEIN(SUBSTRATE-FREE FORM).
1kjo 1KJO CONTAINS THE SAME PROTEIN COMPLEXED WITH Z-L-THREONINE.
1kjp 1KJP CONTAINS THE SAME PROTEIN COMPLEXED WITH Z-L-GLUTAMIC ACID.