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(-) Description

Title :  COCAINE ESTERASE WITH MUTATION L169K, BOUND TO DTT ADDUCT
 
Authors :  J. J. G. Tesmer, M. R. Nance
Date :  29 Jun 09  (Deposition) - 16 Jun 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha/Beta Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Narasimhan, M. R. Nance, D. Gao, M. C. Ko, J. Macdonald, P. Tamburi, D. Yoon, D. M. Landry, J. H. Woods, C. G. Zhan, J. J. Tesmer, R. K. Sunahar
Structural Analysis Of Thermostabilizing Mutations Of Cocaine Esterase.
Protein Eng. Des. Sel. V. 23 537 2010
PubMed-ID: 20436035  |  Reference-DOI: 10.1093/PROTEIN/GZQ025

(-) Compounds

Molecule 1 - COCAINE ESTERASE
    Chains: A
    EC Number: 3.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 22B (+)
    Expression System Strain: BL-21 GOLD (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COCAINE ESTERASE, COCE
    Mutation: YES
    Organism Scientific: RHODOCOCCUS SP. MB1 'BRESLER 1999'
    Organism Taxid: 104109
    Strain: MB1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2DBC1Ligand/Ion(4S,5S)-4,5-BIS(MERCAPTOMETHYL)-1,3-DIOXOLAN-2-OL
3GOL5Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DBC2Ligand/Ion(4S,5S)-4,5-BIS(MERCAPTOMETHYL)-1,3-DIOXOLAN-2-OL
3GOL10Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:298 , ARG A:472BINDING SITE FOR RESIDUE CL A 588
02AC2SOFTWAREARG A:75 , GLY A:82 , GLU A:83 , HOH A:772 , HOH A:942BINDING SITE FOR RESIDUE CL A 589
03AC3SOFTWAREPRO A:354 , ASP A:355 , ARG A:574 , HOH A:626 , HOH A:915BINDING SITE FOR RESIDUE CL A 590
04AC4SOFTWARETRP A:345 , HOH A:1381BINDING SITE FOR RESIDUE CL A 591
05AC5SOFTWARETYR A:44 , SER A:117 , TYR A:118 , TRP A:166 , HIS A:287 , LEU A:407 , GOL A:601 , HOH A:982BINDING SITE FOR RESIDUE DBC A 592
06AC6SOFTWARELEU A:196 , ASN A:197 , VAL A:199 , ARG A:293 , PHE A:408 , HIS A:409 , ASN A:410BINDING SITE FOR RESIDUE GOL A 593
07AC7SOFTWAREASP A:394 , ALA A:396 , LEU A:547 , MET A:550 , HOH A:716 , HOH A:768 , HOH A:769 , HOH A:1182BINDING SITE FOR RESIDUE GOL A 594
08AC8SOFTWAREGLU A:309 , ALA A:310 , ARG A:336 , TRP A:345 , HOH A:937 , HOH A:1116BINDING SITE FOR RESIDUE GOL A 595
09AC9SOFTWAREGLY A:364 , GLY A:365 , SER A:383 , GLY A:384 , THR A:385 , HOH A:823 , HOH A:999 , HOH A:1138 , HOH A:1348BINDING SITE FOR RESIDUE SO4 A 596
10BC1SOFTWAREARG A:556BINDING SITE FOR RESIDUE CL A 597
11BC2SOFTWAREARG A:182BINDING SITE FOR RESIDUE CL A 598
12BC3SOFTWAREHIS A:563 , HOH A:1361BINDING SITE FOR RESIDUE CL A 599
13BC4SOFTWAREARG A:28BINDING SITE FOR RESIDUE CL A 600
14BC5SOFTWARETYR A:44 , SER A:117 , LYS A:169 , DBC A:592 , HOH A:970 , HOH A:984 , HOH A:1181BINDING SITE FOR RESIDUE GOL A 601
15BC6SOFTWARESER A:454 , ALA A:455 , PRO A:469 , ASP A:470 , CYS A:551 , THR A:552 , ALA A:553 , HOH A:645BINDING SITE FOR RESIDUE GOL A 3287

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:149 -Pro A:150
2Thr A:206 -Pro A:207
3Trp A:351 -Pro A:352
4Phe A:529 -Pro A:530

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I2H)

(-) Exons   (0, 0)

(no "Exon" information available for 3I2H)

(-) 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:574
 aligned with COCE_RHOSM | Q9L9D7 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:574
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      574 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571  | 
           COCE_RHOSM     2 VDGNYSVASNVMVPMRDGVRLAVDLYRPDADGPVPVLLVRNPYDKFDVFAWSTQSTNWLEFVRDGYAVVIQDTRGLFASEGEFVPHVDDEADAEDTLSWILEQAWCDGNVGMFGVSYLGVTQWQAAVSGVGGLKAIAPSMASADLYRAPWYGPGGALSVEALLGWSALIGTGLITSRSDARPEDAADFVQLAAILNDVAGAASVTPLAEQPLLGRLIPWVIDQVVDHPDNDESWQSISLFERLGGLATPALITAGWYDGFVGESLRTFVAVKDNADARLVVGPWSHSNLTGRNADRKFGIAATYPIQEATTMHKAFFDRHLRGETDALAGVPKVRLFVMGIDEWRDETDWPLPDTAYTPFYLGGSGAANTSTGGGTLSTSISGTESADTYLYDPADPVPSLGGTLLFHNGDNGPADQRPIHDRDDVLCYSTEVLTDPVEVTGTVSARLFVSSSAVDTDFTAKLVDVFPDGRAIALCDGIVRMRYRETLVNPTLIEAGEIYEVAIDMLATSNVFLPGHRIMVQVSSSNFPKYDRNSNTGGVIAREQLEEMCTAVNRIHRGPEHPSHIVLPIIKR-   -
               SCOP domains d3i2ha1 A:2-351 automated matches                                                                                                                                                                                                                                                                                                                             d3i2ha2 A:352-575 automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 3i2hA01 A:2-145,A:241-348  [code=3.40.50.1820, no name defined]                                                                                 3i2hA02 A:146-240 alpha-amino acid ester hydrolase ( Helical cap domain)                       3i2hA01 A:2-145,A:241-348  [code=3.40.50.1820, no name defined]                                             --------3i2hA03 A:357-575 Galactose-binding domain-like                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeee.....eeeeeeee......hhhhhh....hhhhhhh..eeeeee...............hhhhhhhhhhhhhhhh..eeeeeee.eehhhhhhhhhhhh.....eee..ee..................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhh..hhhhhh.....eeeeeeee..hhhhhhhhhhhhh....eeeeeeeee......ee..ee.hhhhh.hhhhhhhhhhhhhhhhhh...........eeeee....eeeee........eeeeeeee............eee.......eeeeeee........................hhhhh......eee.......eeeeeeeeeeeeeee.....eeeeeeeee.....eeeeeeeeee.hhh..............eeeeeeeeeeeeee....eeeeeee...............hhhhhhhhhh..eeeeeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i2h A   2 VDGNYSVASNVMVPMRDGVRLAVDLYRPDADGPVPVLLVRNPYDKFDVFAWSTQSTNWLEFVRDGYAVVIQDTRGLFASEGEFVPHVDDEADAEDTLSWILEQAWCDGNVGMFGVSYLGVTQWQAAVSGVGGLKAIAPSMASADLYRAPWYGPGGALSVEALLGWSAKIGTGLITSRSDARPEDAADFVQLAAILNDVAGAASVTPLAEQPLLGRLIPWVIDQVVDHPDNDESWQSISLFERLGGLATPALITAGWYDGFVGESLRTFVAVKDNADARLVVGPWSHSNLTGRNADRKFGIAATYPIQEATTMHKAFFDRHLRGETDALAGVPKVRLFVMGIDEWRDETDWPLPDTAYTPFYLGGSGAANTSTGGGTLSTSISGTESADTYLYDPADPVPSLGGTLLFHNGDNGPADQRPIHDRDDVLCYSTEVLTDPVEVTGTVSARLFVSSSAVDTDFTAKLVDVFPDGRAIALCDGIVRMRYRETLVNPTLIEAGEIYEVAIDMLATSNVFLPGHRIMVQVSSSNFPKYDRNSNTGGVIAREQLEEMCTAVNRIHRGPEHPSHIVLPIIKRK 575
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I2H)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (COCE_RHOSM | Q9L9D7)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0008239    dipeptidyl-peptidase activity    Catalysis of the hydrolysis of N-terminal dipeptides from a polypeptide chain.
    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:0050784    cocaine catabolic process    The chemical reactions and pathways resulting in the breakdown of cocaine, an alkaloid obtained from the dried leaves of the shrub Erythroxylon coca. It is a cerebral stimulant and narcotic.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        COCE_RHOSM | Q9L9D7: 1ju3 1ju4 1l7q 1l7r 3i2f 3i2g 3i2i 3i2j 3i2k 3ida 3puh 3pui 4p08

(-) Related Entries Specified in the PDB File

1ju3 WILD-TYPE PROTEIN, IN COMPLEX WITH TRANSITION STATE ANALOG.
1ju4 WILD-TYPE PROTEIN, IN COMPLEX WITH PRODUCT.
1l7q COCAINE ESTERASE, WITH MUTATION S117A.
1l7r COCAINE ESTERASE, WITH MUTATION Y44F.
3i2f
3i2g
3i2i
3i2j
3i2k