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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI LYSOPHOSPHOLIASE L1/ACYL-COA THIOESTERASE I/PROTEASE I L109P MUTANT
 
Authors :  Y. -C. Lo, S. -C. Lin, J. -F. Shaw, Y. -C. Liaw
Date :  14 Aug 01  (Deposition) - 08 Jul 03  (Release) - 06 May 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hydrolase, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -C. Lo, S. -C. Lin, J. -F. Shaw, Y. -C. Liaw
Crystal Structure Of Escherichia Coli Thioesterase I/Protease I/Lysophospholipase L1: Consensus Sequence Blocks Constitute The Catalytic Center Of Sgnh-Hydrolases Through A Conserved Hydrogen Bond Network
J. Mol. Biol. V. 330 539 2003
PubMed-ID: 12842470  |  Reference-DOI: 10.1016/S0022-2836(03)00637-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACYL-COA THIOESTERASE I
    Chains: A
    EC Number: 3.1.2.-, 3.1.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-20B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TESA, APEA, PLDC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PROTEASE I, LYSOPHOSPHOLIPASE L1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:17 , SER A:18 , ALA A:21 , ILE A:42 , ARG A:53 , LEU A:57 , ARG A:160 , HOH A:1029 , HOH A:1047BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWARELYS A:34 , THR A:35 , VAL A:178 , HOH A:1166BINDING SITE FOR RESIDUE IMD A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_GDSL_SERPS01098 Lipolytic enzymes 'G-D-S-L' family, serine active site.TESA_ECOL630-40  1A:4-14
TESA_ECOLI30-40  1A:4-14
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_GDSL_SERPS01098 Lipolytic enzymes 'G-D-S-L' family, serine active site.TESA_ECOL630-40  1A:4-14
TESA_ECOLI30-40  1A:4-14
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_GDSL_SERPS01098 Lipolytic enzymes 'G-D-S-L' family, serine active site.TESA_ECOL630-40  2A:4-14
TESA_ECOLI30-40  2A:4-14

(-) Exons   (0, 0)

(no "Exon" information available for 1JRL)

(-) 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:178
 aligned with TESA_ECOL6 | P0ADA2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:179
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196         
           TESA_ECOL6    27 ADTLLILGDSLSAGYRMSASAAWPALLNDKWQSKTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRLPANYGRRYNEAFSAIYPKLAKEFDVPLLPFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQPLVN 205
               SCOP domains d1jrla_ A: Thioesterase I, TAP                                                                                                                                                      SCOP domains
               CATH domains 1jrlA00 A:1-179  [code=3.40.50. 1110, no name defined]                                                                                                                              CATH domains
               Pfam domains ---Lipase_GDSL-1jrlA01 A:4-170                                                                                                                                            --------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhh...hhhhhhhhhhhhhh-..eeeee......hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LIPASE_GDSL--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrl A   1 ADTLLILGDSLSAGYRMSASAAWPALLNDKW-SKTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRPPANYGRRYNEAFSAIYPKLAKEFDVPLLPFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQPLVN 179
                                    10        20        30| |     40        50        60        70        80        90       100       110       120       130       140       150       160       170         
                                                         31 |                                                                                                                                                  
                                                           33                                                                                                                                                  


Chain A from PDB  Type:PROTEIN  Length:178
 aligned with TESA_ECOLI | P0ADA1 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:179
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196         
           TESA_ECOLI    27 ADTLLILGDSLSAGYRMSASAAWPALLNDKWQSKTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRLPANYGRRYNEAFSAIYPKLAKEFDVPLLPFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQPLVN 205
               SCOP domains d1jrla_ A: Thioesterase I, TAP                                                                                                                                                      SCOP domains
               CATH domains 1jrlA00 A:1-179  [code=3.40.50. 1110, no name defined]                                                                                                                              CATH domains
               Pfam domains ---Lipase_GDSL-1jrlA01 A:4-170                                                                                                                                            --------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhh...hhhhhhhhhhhhhh-..eeeee......hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---LIPASE_GDSL--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrl A   1 ADTLLILGDSLSAGYRMSASAAWPALLNDKW-SKTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRPPANYGRRYNEAFSAIYPKLAKEFDVPLLPFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQPLVN 179
                                    10        20        30| |     40        50        60        70        80        90       100       110       120       130       140       150       160       170         
                                                         31 |                                                                                                                                                  
                                                           33
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SGNH_hydrolase (17)

(-) Gene Ontology  (12, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (TESA_ECOL6 | P0ADA2)
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:0016298    lipase activity    Catalysis of the hydrolysis of a lipid or phospholipid.
    GO:0004622    lysophospholipase activity    Catalysis of the reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate.
    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:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (TESA_ECOLI | P0ADA1)
molecular function
    GO:0047617    acyl-CoA hydrolase activity    Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016298    lipase activity    Catalysis of the hydrolysis of a lipid or phospholipid.
    GO:0004622    lysophospholipase activity    Catalysis of the reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate.
    GO:0016290    palmitoyl-CoA hydrolase activity    Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate.
    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.
    GO:0004620    phospholipase activity    Catalysis of the hydrolysis of a glycerophospholipid.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1jrl
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  TESA_ECOLI | P0ADA1
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 Related Entries

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

UniProtKB/Swiss-Prot
        TESA_ECOL6 | P0ADA2: 1ivn 1j00 1u8u 1v2g
        TESA_ECOLI | P0ADA1: 1ivn 1j00 1u8u 1v2g 5tic 5tid 5tie 5tif

(-) Related Entries Specified in the PDB File

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