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(-) Description

Title :  CRYSTAL STRUCTURE OF A THERMOSTABLE ESTERASE
 
Authors :  M. Levisson, L. Sun, S. Hendriks, B. W. Dijkstra, J. Van Der Oost, S. W. M. Kengen
Date :  04 Jul 08  (Deposition) - 17 Feb 09  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Alpha-Beta Hydrolase, Beta Sheet (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Levisson, L. Sun, S. Hendriks, P. Swinkels, T. Akveld, J. B. Bultema, A. Barendregt, R. H. H. Van Den Heuvel, B. W. Dijkstra, J. Van Der Oost, S. W. M. Kengen
Crystal Structure And Biochemical Properties Of A Novel Thermostable Esterase Containing An Immunoglobulin-Like Domain.
J. Mol. Biol. V. 385 949 2009
PubMed-ID: 19013466  |  Reference-DOI: 10.1016/J.JMB.2008.10.075
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTERASE
    Chains: A, B
    EC Number: 3.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 16-395
    Gene: TM_0033
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 30)
No.NameCountTypeFull Name
1SO430Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:116 , GLY A:197 , ALA A:198 , GLY A:199 , SER A:286 , MET A:287 , HIS A:374BINDING SITE FOR RESIDUE SO4 A 400
02AC2SOFTWARELYS A:29 , ARG A:222 , GLU A:332 , GLU A:362 , LYS A:363BINDING SITE FOR RESIDUE SO4 A 401
03AC3SOFTWARELYS A:61 , SER A:69 , SER A:70 , ASP B:56BINDING SITE FOR RESIDUE SO4 A 402
04AC4SOFTWARELYS A:152 , LEU A:154 , ILE A:155 , ASP A:157 , ASP A:158BINDING SITE FOR RESIDUE SO4 A 403
05AC5SOFTWAREHIS A:153 , ASP A:157 , ARG A:176 , TYR A:206BINDING SITE FOR RESIDUE SO4 A 404
06AC6SOFTWAREPHE B:116 , GLY B:197 , ALA B:198 , GLY B:199 , SER B:286 , MET B:287 , HIS B:374BINDING SITE FOR RESIDUE SO4 B 500
07AC7SOFTWARELYS B:29 , ARG B:222 , GLU B:332 , GLU B:362 , LYS B:363BINDING SITE FOR RESIDUE SO4 B 501
08AC8SOFTWAREASP A:56 , SER B:69 , SER B:70BINDING SITE FOR RESIDUE SO4 A 502
09AC9SOFTWARELYS B:152 , LEU B:154 , ILE B:155 , ASP B:157 , ASP B:158BINDING SITE FOR RESIDUE SO4 B 503
10BC1SOFTWAREHIS B:153 , ILE B:156 , ASP B:157 , ARG B:176BINDING SITE FOR RESIDUE SO4 B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:64 -Gly A:65
2Pro A:114 -Asn A:115
3Gly A:138 -Asn A:139
4Arg B:92 -Gly B:93
5Pro B:167 -Glu B:168
6Thr B:169 -Gly B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DOH)

(-) 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:375
 aligned with Q9WXP0_THEMA | Q9WXP0 from UniProtKB/TrEMBL  Length:395

    Alignment length:375
                                    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       320       330       340       350       360       370       380       390     
         Q9WXP0_THEMA    21 VKSVTLITKVFPEGEKVCAVVIEYPVEIDGQKLSPDQFSVKVKTGDTYSSRTITKVYANNSGGLSFSIFNNRGKYVVLELSTEDLHSNTIVFGPNFLNTRMKLDYIVSQLVPIFDVDGNEVEPFTSKQTDEKHLIIDDFLAFTFKDPETGVEIPYRLFVPKDVNPDRKYPLVVFLHGAGERGTDNYLQVAGNRGAVVWAQPRYQVVHPCFVLAPQCPPNSSWSTLFTDRENPFNPEKPLLAVIKIIRKLLDEYNIDENRIYITGLSMGGYGTWTAIMEFPELFAAAIPICGGGDVSKVERIKDIPIWVFHAEDDPVVPVENSRVLVKKLAEIGGKVRYTEYEKGFMEKHGWDPHGSWIPTYENQEAIEWLFEQSR 395
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeeeeeeeeeeee.hhhhhh.eeeeee....eeee.eeeeeee............eeeeeeeee...hhhhh................eeeee..............eeee..eeeeehhh.eeeeeee......eeeeeee..........eeeeeee.hhhhh....hhhhhh....hhhhhhhhhh....eeeee.....................hhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh...eeeeee..hhhhhh......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3doh A  21 VKSVTLITKVFPEGEKVCAVVIEYPVEIDGQKLSPDQFSVKVKTGDTYSSRTITKVYANNSGGLSFSIFNNRGKYVVLELSTEDLHSNTIVFGPNFLNTRMKLDYIVSQLVPIFDVDGNEVEPFTSKQTDEKHLIIDDFLAFTFKDPETGVEIPYRLFVPKDVNPDRKYPLVVFLHGAGERGTDNYLQVAGNRGAVVWAQPRYQVVHPCFVLAPQCPPNSSWSTLFTDRENPFNPEKPLLAVIKIIRKLLDEYNIDENRIYITGLSMGGYGTWTAIMEFPELFAAAIPICGGGDVSKVERIKDIPIWVFHAEDDPVVPVENSRVLVKKLAEIGGKVRYTEYEKGFMEKHGWDPHGSWIPTYENQEAIEWLFEQSR 395
                                    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       320       330       340       350       360       370       380       390     


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with Q9WXP0_THEMA | Q9WXP0 from UniProtKB/TrEMBL  Length:395

    Alignment length:375
                                    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       320       330       340       350       360       370       380       390     
         Q9WXP0_THEMA    21 VKSVTLITKVFPEGEKVCAVVIEYPVEIDGQKLSPDQFSVKVKTGDTYSSRTITKVYANNSGGLSFSIFNNRGKYVVLELSTEDLHSNTIVFGPNFLNTRMKLDYIVSQLVPIFDVDGNEVEPFTSKQTDEKHLIIDDFLAFTFKDPETGVEIPYRLFVPKDVNPDRKYPLVVFLHGAGERGTDNYLQVAGNRGAVVWAQPRYQVVHPCFVLAPQCPPNSSWSTLFTDRENPFNPEKPLLAVIKIIRKLLDEYNIDENRIYITGLSMGGYGTWTAIMEFPELFAAAIPICGGGDVSKVERIKDIPIWVFHAEDDPVVPVENSRVLVKKLAEIGGKVRYTEYEKGFMEKHGWDPHGSWIPTYENQEAIEWLFEQSR 395
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeeeeee.....hhhhhhhh.eeeeeee..eeeee.eeeeeee...............eeeeee...hhhhh.ee.......ee....eeeee...ee.....ee..eeee..eeee......eeeeee......eeeeeee..........eeeeeee..........hhhhhh....hhhhhhhhhh....eeeee..............--.....hhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh...eeeeee..hhhhhh......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3doh B  21 VKSVTLITKVFPEGEKVCAVVIEYPVEIDGQKLSPDQFSVKVKTGDTYSSRTITKVYANNSGGLSFSIFNNRGKYVVLELSTEDLHSNTIVFGPNFLNTRMKLDYIVSQLVPIFDVDGNEVEPFTSKQTDEKHLIIDDFLAFTFKDPETGVEIPYRLFVPKDVNPDRKYPLVVFLHGAGERGTDNYLQVAGNRGAVVWAQPRYQVVHPCFVLAPQCPPNSSWSTLFTD--NPFNPEKPLLAVIKIIRKLLDEYNIDENRIYITGLSMGGYGTWTAIMEFPELFAAAIPICGGGDVSKVERIKDIPIWVFHAEDDPVVPVENSRVLVKKLAEIGGKVRYTEYEKGFMEKHGWDPHGSWIPTYENQEAIEWLFEQSR 395
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       | -|      260       270       280       290       300       310       320       330       340       350       360       370       380       390     
                                                                                                                                                                                                                                                             248  |                                                                                                                                                
                                                                                                                                                                                                                                                                251
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WXP0_THEMA | Q9WXP0)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    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:0008474    palmitoyl-(protein) hydrolase activity    Catalysis of the reaction: palmitoyl-protein + H2O = palmitate + protein.
biological process
    GO:0002084    protein depalmitoylation    The removal of palymitoyl groups from a lipoprotein.
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

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        Q9WXP0_THEMA | Q9WXP0: 3doi

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3doi