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(-) Description

Title :  THERMOLYSIN (60% ACETONE SOAKED CRYSTALS)
 
Authors :  A. C. English, C. R. Groom, R. E. Hubbard
Date :  08 Aug 00  (Deposition) - 18 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloproteinase, Organic Solvent, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. English, C. R. Groom, R. E. Hubbard
Experimental And Computational Mapping Of The Binding Surface Of A Crystalline Protein.
Protein Eng. V. 14 47 2001
PubMed-ID: 11287678  |  Reference-DOI: 10.1093/PROTEIN/14.1.47
(for further references see the PDB file header)

(-) 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, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ACN5Ligand/IonACETONE
2CA4Ligand/IonCALCIUM ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4ZN1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:142 , HIS A:146 , GLU A:166 , HOH A:512BINDING SITE FOR RESIDUE ZN A 500
02AC2SOFTWAREASP A:138 , GLU A:177 , ASP A:185 , GLU A:187 , GLU A:190 , HOH A:523BINDING SITE FOR RESIDUE CA A 501
03AC3SOFTWAREGLU A:177 , ASN A:183 , ASP A:185 , GLU A:190 , HOH A:522 , HOH A:539BINDING SITE FOR RESIDUE CA A 502
04AC4SOFTWAREASP A:57 , ASP A:59 , GLN A:61 , HOH A:525 , HOH A:536 , HOH A:556BINDING SITE FOR RESIDUE CA A 503
05AC5SOFTWARETYR A:193 , THR A:194 , ILE A:197 , ASP A:200 , HOH A:547 , HOH A:574BINDING SITE FOR RESIDUE CA A 504
06AC6SOFTWAREHIS A:216 , SER A:218 , TYR A:251BINDING SITE FOR RESIDUE DMS A 505
07AC7SOFTWAREHIS A:142 , ARG A:203BINDING SITE FOR RESIDUE ACN A 506
08AC8SOFTWARETYR A:84 , SER A:92 , TYR A:93 , ILE A:100 , LEU A:144 , VAL A:148BINDING SITE FOR RESIDUE ACN A 507
09AC9SOFTWARETYR A:27 , ALA A:56 , GLY A:212 , PRO A:214 , LYS A:219 , HOH A:592 , HOH A:643BINDING SITE FOR RESIDUE ACN A 508
10BC1SOFTWAREGLY A:248 , THR A:249 , VAL A:255 , GLN A:273 , LEU A:275 , THR A:276 , HOH A:615BINDING SITE FOR RESIDUE ACN A 509
11BC2SOFTWAREGLN A:108BINDING SITE FOR RESIDUE ACN A 510

(-) SS Bonds  (0, 0)

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

(-) 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 1FJO)

(-) 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 1FJO)

(-) 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:316
 aligned with THER_BACTH | P00800 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:316
                                   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 548
               SCOP domains d1fjoa_ A: Thermolysin                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -----1fjoA01 A:6-154  [code=3.10.170.10, no name defined]                                                                                                 1fjoA02 A:155-315 Neutral Protease Domain 2                                                                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1fjo A   1 ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGDGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSEMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVK 316
                                    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
   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FJO)

(-) 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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  1fjo
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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 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 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

1fj3 THERMOLYSIN (50% 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)
1tli 1TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
2tli 2TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
3tli 3TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
4tli 4TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
5tli 5TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
6tli 6TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
7tli 7TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.
8tli 8TLI FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/SOLUTES.