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(-) Description

Title :  CRYSTAL STRUCTURE HORMONE-SENSITIVE LIPASE FROM A METAGENOME LIBRARY
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  02 Jul 08  (Deposition) - 13 Jan 09  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (2x),D (2x)
Biol. Unit 6:  B,C  (2x)
Keywords :  Alpha/Beta Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Nam, M. -Y. Kim, S. -J. Kim, A. Priyadarshi, S. -T. Kwon, B. -S. Koo, S. -H. Yoon, K. Y. Hwang
Structural And Functional Analysis Of A Novel Hormone-Sensitive Lipase From A Metagenome Library
Proteins V. 74 1036 2008
PubMed-ID: 19089974  |  Reference-DOI: 10.1002/PROT.22313
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTERASE/LIPASE
    Chains: A, B, C, D
    EC Number: 3.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ESTE7
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133
    Other Details: THIS PROTEIN WAS PURIFIED FROM METAGENOME LIBRARY(SOIL UNCULTURED BACTERIA)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (2x): A (2x)  D (2x)
Biological Unit 6 (2x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2SO414Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO47Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2SO43Ligand/IonSULFATE ION
Biological Unit 5 (2, 8)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2SO46Ligand/IonSULFATE ION
Biological Unit 6 (2, 22)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2SO418Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:90 , SER A:157 , LEU A:206 , HIS A:281BINDING SITE FOR RESIDUE BME A 325
02AC2SOFTWAREALA A:55 , GLU A:56 , GLN A:105 , LYS A:108BINDING SITE FOR RESIDUE SO4 A 323
03AC3SOFTWAREARG A:194 , TYR A:234 , ARG A:263 , TRP B:195BINDING SITE FOR RESIDUE SO4 A 324
04AC4SOFTWARESER B:157 , LEU B:206 , HIS B:281 , HOH B:385BINDING SITE FOR RESIDUE BME B 330
05AC5SOFTWAREALA B:55 , GLU B:56 , GLN B:105 , LYS B:108BINDING SITE FOR RESIDUE SO4 B 323
06AC6SOFTWARETHR A:258 , THR A:259 , GLU A:262 , THR B:258 , THR B:259 , GLU B:262BINDING SITE FOR RESIDUE SO4 B 324
07AC7SOFTWAREARG B:194 , LYS B:226 , TYR B:234 , ARG B:263BINDING SITE FOR RESIDUE SO4 B 325
08AC8SOFTWAREARG B:19 , LEU B:22 , GLN B:23BINDING SITE FOR RESIDUE SO4 B 326
09AC9SOFTWAREASP B:39 , GLN B:40 , ASP C:118 , LEU C:121 , HOH C:371BINDING SITE FOR RESIDUE SO4 B 327
10BC1SOFTWAREASP B:118 , TYR B:119 , ARG B:120BINDING SITE FOR RESIDUE SO4 B 328
11BC2SOFTWAREASP B:64 , THR B:144 , HOH B:378 , HOH B:379BINDING SITE FOR RESIDUE SO4 B 329
12BC3SOFTWAREGLY C:90 , SER C:157 , ALA C:207 , MET C:215 , HIS C:281 , HOH C:359BINDING SITE FOR RESIDUE BME C 325
13BC4SOFTWAREGLU C:56 , GLN C:105 , LYS C:108BINDING SITE FOR RESIDUE SO4 C 323
14BC5SOFTWAREARG C:194 , TYR C:234 , ARG C:263BINDING SITE FOR RESIDUE SO4 C 324
15BC6SOFTWARESER D:157 , LEU D:206 , MET D:215 , HIS D:281BINDING SITE FOR RESIDUE BME D 326
16BC7SOFTWAREALA D:55 , GLU D:56 , GLN D:105 , LYS D:108BINDING SITE FOR RESIDUE SO4 D 323
17BC8SOFTWAREARG D:194 , TYR D:234 , ARG D:263BINDING SITE FOR RESIDUE SO4 D 324
18BC9SOFTWAREMET D:177BINDING SITE FOR RESIDUE SO4 D 325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DNM)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:122 -Pro A:123
2Phe A:127 -Pro A:128
3Ala B:122 -Pro B:123
4Phe B:127 -Pro B:128
5Ala C:122 -Pro C:123
6Phe C:127 -Pro C:128
7Ala D:122 -Pro D:123
8Phe D:127 -Pro D:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DNM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DNM)

(-) Exons   (0, 0)

(no "Exon" information available for 3DNM)

(-) 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:297
 aligned with Q0GMU1_9BACT | Q0GMU1 from UniProtKB/TrEMBL  Length:309

    Alignment length:297
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       
         Q0GMU1_9BACT    13 DTKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARIS 309
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........eeeeeee..eeeeeee.......eeeee............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhh......eeee.........hhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnm A  13 DTKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARIS 309
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with Q0GMU1_9BACT | Q0GMU1 from UniProtKB/TrEMBL  Length:309

    Alignment length:296
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302      
         Q0GMU1_9BACT    13 DTKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh........eee..ee..eeeeeee.......eeeee............hhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhh......eeeee.........hhhhhhhhhhh...hhhhhh..hhhhhh.........hhhhh.......eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnm B  13 DTKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302      


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with Q0GMU1_9BACT | Q0GMU1 from UniProtKB/TrEMBL  Length:309

    Alignment length:295
                                    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     
         Q0GMU1_9BACT    14 TKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.----...hhhhhhhhhh........eeeeeeee..eeeeeeee......eeeee.........hhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh.....eeeee.........hhhhhhh.......hhhhhhhhhhhhhh.........hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnm C  14 TKMDPRDFLQLLKINAEKA----PLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
                                    23        |-   |    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     
                                             32   37                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:291
 aligned with Q0GMU1_9BACT | Q0GMU1 from UniProtKB/TrEMBL  Length:309

    Alignment length:294
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
         Q0GMU1_9BACT    15 KMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee......eeeee............hhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhh......eeeee..........hhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhh.......eeeeeeee..hhhhhhhhhhhhhh....eeeeeeeeee.hhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dnm D  15 KMDPRDFLQLLKINAEKA---LPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARI 308
                                    24       | - |      44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
                                            32  36
   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  (0, 0)

(no "SCOP Domain" information available for 3DNM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DNM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DNM)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q0GMU1_9BACT | Q0GMU1)
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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  Cis Peptide Bonds
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  3dnm
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 Related Entries

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

UniProtKB/TrEMBL
        Q0GMU1_9BACT | Q0GMU1: 3k6k

(-) Related Entries Specified in the PDB File

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