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(-) Description

Title :  DIPEPTIDE INHIBITORS OF THERMOLYSIN
 
Authors :  B. A. Lund, I. Leiros, H. -K. S. Leiros
Date :  07 May 09  (Deposition) - 12 May 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase-Inhibitor Complex, Dipeptide Inhibitors, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Lund, I. Leiros, H. -K. S. Leiros
Dipeptide Inhibitors Of Thermolysin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THERMOLYSIN
    Chains: A
    EC Number: 3.4.24.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS THERMOPROTEOLYTICUS
    Organism Taxid: 1427
    Other Details: THE DI-PEPTIDE IY IS BOUND TO THE PROTEIN
    Synonym: THERMOSTABLE NEUTRAL PROTEINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2ILE1Mod. Amino AcidISOLEUCINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4TYR1Mod. Amino AcidTYROSINE
5ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:142 , HIS A:146 , GLU A:166 , HOH A:2351BINDING SITE FOR RESIDUE ZN A1317
2AC2SOFTWAREASP A:138 , GLU A:177 , ASP A:185 , GLU A:187 , GLU A:190 , HOH A:2232BINDING SITE FOR RESIDUE CA A1318
3AC3SOFTWAREGLU A:177 , ASN A:183 , ASP A:185 , GLU A:190 , HOH A:2240 , HOH A:2241BINDING SITE FOR RESIDUE CA A1319
4AC4SOFTWAREASP A:57 , ASP A:59 , GLN A:61 , HOH A:2109 , HOH A:2112 , HOH A:2128BINDING SITE FOR RESIDUE CA A1320
5AC5SOFTWARETYR A:193 , THR A:194 , ILE A:197 , ASP A:200 , HOH A:2236 , HOH A:2243BINDING SITE FOR RESIDUE CA A1321
6AC6SOFTWAREASN A:112 , ALA A:113 , HIS A:142 , GLU A:143 , ARG A:203 , HIS A:231 , TYR A:1002 , HOH A:2351BINDING SITE FOR RESIDUE ILE A1001
7AC7SOFTWAREASN A:111 , ASN A:112 , PHE A:130 , HIS A:231 , ILE A:1001 , PEG A:1324 , HOH A:2352 , HOH A:2353BINDING SITE FOR RESIDUE TYR A1002
8AC8SOFTWAREGLY A:109 , TYR A:110 , ASN A:111 , ASN A:112 , GLN A:158 , TYR A:1002 , HOH A:2186 , HOH A:2187BINDING SITE FOR RESIDUE PEG A1324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WHZ)

(-) 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 2WHZ)

(-) 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 2WHZ)

(-) 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:318
 aligned with THER_BACTH | P00800 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:318
                                                                                                                                                                                                                                                                                                                                                     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 d2whza_ A: Thermolysin                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---Peptidase_M4-2whzA01 A:4-151                                                                                                                        -Peptidase_M4_C-2whzA02 A:153-315                                                                                                                                   --- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeee...ee.ee......eeeee.........ee.ee...ee....hhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee......eee....eeee........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
                2whz A    1 ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVKIY 1002
                                    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| 
                                                                                                                                                                                                                                                                                                                                                     1001
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WHZ)

(-) 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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  2whz
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  THER_BACTH | P00800
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  3.4.24.27
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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 1kkk 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 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

1fj3 THERMOLYSIN (50% ACETONE SOAKED)
1fjo THERMOLYSIN (60% ACETONE SOAKED CRYSTALS)
1fjq THERMOLYSIN (70% ACETONE SOAKED CRYSTALS)
1fjt THERMOLYSIN (50% ACETONITRILE SOAKED CRYSTALS)
1fju THERMOLYSIN (80% ACETONITRILE SOAKED CRYSTALS)
1fjv THERMOLYSIN (60% ACETONITRILE SOAKED CRYSTALS)
1fjw THERMOLYSIN (50 MM PHENOL SOAKED)
1gxw THE 2.2 A RESOLUTION STRUCTURE OF THERMOLYSIN CRYSTALLIZED IN PRESENCE OF POTASSIUM THIOCYANATE
1hyt THERMOLYSIN COMPLEXED WITH BENZYLSUCCINIC ACID (2(S)-BENZYL-3-CARBOXYPROPIONIC ACID)
1kei THERMOLYSIN (SUBSTRATE-FREE)
1kjo THERMOLYSIN COMPLEXED WITH Z-L-THREONINE ( BENZYLOXYCARBONYL-L-THREONINE)
1kjp THERMOLYSIN COMPLEXED WITH Z-L-GLUTAMIC ACID (BENZYLOXYCARBONYL-L-GLUTAMIC ACID)
1kkk THERMOLYSIN COMPLEXED WITH Z-L-ASPARTIC ACID (BENZYLOXYCARBONYL-L-ASPARTIC ACID)
1kl6 THERMOLYSIN COMPLEXED WITH Z-L-ALANINE ( BENZYLOXYCARBONYL-L-ALANINE)
1kr6 THERMOLYSIN COMPLEXED WITH Z-D-GLUTAMIC ACID (BENZYLOXYCARBONYL-D-GLUTAMIC ACID)
1kro THERMOLYSIN COMPLEXED WITH Z-D-THREONINE ( BENZYLOXYCARBONYL-D-THREONINE)
1ks7 THERMOLYSIN COMPLEXED WITH Z-D-ASPARTIC ACID (BENZYLOXYCARBONYL-D-ASPARTIC ACID)
1kto THERMOLYSIN COMPLEXED WITH Z-D-ALANINE ( BENZYLOXYCARBONYL-D-ALANINE)
1l3f THERMOLYSIN IN THE ABSENCE OF SUBSTRATE HAS AN OPENCONFORMATION
1lna THERMOLYSIN COMPLEXED WITH COBALT
1lnb THERMOLYSIN COMPLEXED WITH IRON
1lnc THERMOLYSIN COMPLEXED WITH MANGANESE
1lnd THERMOLYSIN COMPLEXED WITH ZINC
1lne THERMOLYSIN COMPLEXED WITH CADMIUM
1lnf THERMOLYSIN
1os0 THERMOLYSIN WITH AN ALPHA-AMINO PHOSPHINIC INHIBITOR
1pe5 THERMOLYSIN WITH TRICYCLIC INHIBITOR
1pe7 THERMOLYSIN WITH BICYCLIC INHIBITOR
1pe8 THERMOLYSIN WITH MONOCYCLIC INHIBITOR
1qf0 THERMOLYSIN COMPLEXED WITH (2-SULPHANYL-3- PHENYLPROPANOYL)-PHE-TYR. PARAMETERS FOR ZN- BIDENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE
1qf1 THERMOLYSIN COMPLEXED WITH (2- SULPHANYLHEPTANOYL)-PHE-ALA. PARAMETERS FOR ZN -BIDENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE
1qf2 THERMOLYSIN COMPLEXED WITH (2-SULPHANYL-3- PHENYLPROPANOYL)-GLY-(5-PHENYLPROLINE). PARAMETERS FOR ZN- MONODENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE
1thl THERMOLYSIN COMPLEXED WITH A NOVEL GLUTARAMIDE DERIVATIVE, N-(1-(2(R,S)-CARBOXY-4- PHENYLBUTYL) CYCLOPENTYLCARBONYL)-(S)-TRYPTOPHAN
1tli THERMOLYSIN (2% ISOPROPANOL SOAKED CRYSTALS)
1tlp THERMOLYSIN COMPLEX WITH PHOSPHORAMIDON
1tlx THERMOLYSIN (NATIVE)
1tmn THERMOLYSIN COMPLEX WITH N-(1-CARBOXY-3- PHENYLPROPYL)-L-LEUCYL-L-TRYPTOPHAN
1trl THERMOLYSIN FRAGMENT 255 - 316 (NMR, 8 STRUCTURES)
1y3g CRYSTAL STRUCTURE OF A SILANEDIOL PROTEASE INHIBITOR BOUNDTO THERMOLYSIN
1z9g CRYSTAL STRUCTURE ANALYSIS OF THERMOLYSIN COMPLEXED WITHTHE INHIBITOR (R)-RETRO- THIORPHAN
1zdp CRYSTAL STRUCTURE ANALYSIS OF THERMOLYSIN COMPLEXED WITHTHE INHIBITOR (S)-THIORPHAN
2a7g ON THE ROUTINE USE OF SOFT X-RAYS IN MACROMOLECULARCRYSTALLOGRAPHY, PART III- THE OPTIMAL DATA COLLECTIONWAVELENGTH
2tli THERMOLYSIN (5% ISOPROPANOL SOAKED CRYSTALS)
2tlx THERMOLYSIN (NATIVE)
2tmn THERMOLYSIN COMPLEX WITH N-PHOSPHORYL-L- LEUCINAMIDE (P-LEU-NH2)
2wi0 DIPEPTIDE INHIBITORS OF THERMOLYSIN
3tli THERMOLYSIN (10% ISOPROPANOL SOAKED CRYSTALS)
3tmn THERMOLYSIN COMPLEX WITH VAL-TRP (VW)
4tli THERMOLYSIN (25% ISOPROPANOL SOAKED CRYSTALS)
4tln THERMOLYSIN COMPLEX WITH L-LEUCYL- HYDROXYLAMINE
4tmn THERMOLYSIN COMPLEX WITH CBZ-PHE==P==-LEU- ALA (ZFPLA)
5tli THERMOLYSIN (60% ISOPROPANOL SOAKED CRYSTALS)
5tln THERMOLYSIN COMPLEX WITH HONH-BENZYLMALONYL-L -ALANYLGLYCINE-P-NITROANILIDE
5tmn THERMOLYSIN COMPLEX WITH CBZ-GLY==P==-LEU- LEU (ZG==P==LL)
6tli THERMOLYSIN (60% ISOPROPANOL SOAKED CRYSTALS)
6tmn THERMOLYSIN COMPLEX WITH CBZ-GLY==P==-(O)- LEU-LEU (ZG==P==(O)LL)
7tli THERMOLYSIN (90% ISOPROPANOL SOAKED CRYSTALS)
7tln THERMOLYSIN COMPLEX WITH CH2CO(N-OH)LEU- OCH3
8tli THERMOLYSIN (100% ISOPROPANOL SOAKED CRYSTALS)
8tln THERMOLYSIN COMPLEXED WITH VAL-LYS DIPEPTIDE