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(-) Description

Title :  PYROBACULUM CALIDIFONTIS ESTERASE MONOCLINIC FORM
 
Authors :  G. J. Palm, X. Bogdanovic, W. Hinrichs
Date :  27 Apr 11  (Deposition) - 18 May 11  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hyperthermophilic Enzyme, Hydrolase, Tertiary Alcohol, Alpha/Beta Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. J. Palm, E. Fernandez-Alvaro, X. Bogdanovic, S. Bartsch, J. Sczodrok, R. K. Singh, D. Boettcher, H. Atomi, U. T. Bornscheuer, W. Hinrichs
The Crystal Structure Of An Esterase Fom The Hyperthermophilic Microorganism Pyrobaculum Calidifontis Va1 Supports Explanation Of Its Enantioselectivity.
Appl. Microbiol. Biotechnol. V. 91 1061 2011
PubMed-ID: 21614503  |  Reference-DOI: 10.1007/S00253-011-3337-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTERASE
    ChainsA, B, C, D
    EC Number3.1.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificPYROBACULUM CALIDIFONTIS
    Organism Taxid181486
    SynonymALPH-BETA HYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:139 , ASN A:140 , TYR A:141 , ASP A:142 , LYS A:143BINDING SITE FOR RESIDUE SO4 A1314
2ASAAUTHORSER A:157 , HIS A:284 , ASP A:254CATALYTIC TRIAD IN MONOMER A
3ASBAUTHORSER B:157 , HIS B:284 , ASP B:254CATALYTIC TRIAD IN MONOMER B
4ASCAUTHORSER C:157 , HIS C:284 , ASP C:254CATALYTIC TRIAD IN MONOMER C
5ASDAUTHORSER D:157 , HIS D:284 , ASP D:254CATALYTIC TRIAD IN MONOMER D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YH2)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:118 -Pro A:119
2Phe A:123 -Pro A:124
3Ala B:118 -Pro B:119
4Phe B:123 -Pro B:124
5Ala C:118 -Pro C:119
6Phe C:123 -Pro C:124
7Ala D:118 -Pro D:119
8Phe D:123 -Pro D:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YH2)

(-) Exons   (0, 0)

(no "Exon" information available for 2YH2)

(-) 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:308
 aligned with Q8NKS0_9CREN | Q8NKS0 from UniProtKB/TrEMBL  Length:313

    Alignment length:313
                                    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   
         Q8NKS0_9CREN     1 MPLSPILRQILQQLAAQLQFRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
               SCOP domains d2yh2a_ A: aut     omated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..-----.....hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee........eeeee............hhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yh2 A   1 MPLSPILRQILQQL-----FRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
                                    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   
                                        14    20                                                                                                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:307
 aligned with Q8NKS0_9CREN | Q8NKS0 from UniProtKB/TrEMBL  Length:313

    Alignment length:312
                                    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  
         Q8NKS0_9CREN     2 PLSPILRQILQQLAAQLQFRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
               SCOP domains d2yh2b_ B: a     utomated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.-----......hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee......eeeeeee............hhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeehhhhhhhhhhhhhhhhh......eeeee..........hhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yh2 B   2 PLSPILRQILQQ-----QFRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
                                    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  
                                      13    19                                                                                                                                                                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:305
 aligned with Q8NKS0_9CREN | Q8NKS0 from UniProtKB/TrEMBL  Length:313

    Alignment length:312
                                    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  
         Q8NKS0_9CREN     2 PLSPILRQILQQLAAQLQFRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
               SCOP domains d2yh2c_ C: auto       mated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh-------.hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee......eeeeeee.........hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeehhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yh2 C   2 PLSPILRQILQQLAA-------MDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
                                    11    |    -  |     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  
                                         16      24                                                                                                                                                                                                                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:307
 aligned with Q8NKS0_9CREN | Q8NKS0 from UniProtKB/TrEMBL  Length:313

    Alignment length:312
                                    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  
         Q8NKS0_9CREN     2 PLSPILRQILQQLAAQLQFRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
               SCOP domains d2yh2d_ D: au     tomated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------Abhydrolase_3-2yh2D01 D:79-288                                                                                                                                                                                    ------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------Abhydrolase_3-2yh2D02 D:79-288                                                                                                                                                                                    ------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------Abhydrolase_3-2yh2D03 D:79-288                                                                                                                                                                                    ------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------Abhydrolase_3-2yh2D04 D:79-288                                                                                                                                                                                    ------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhh.-----.....hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee......eeeeeee.........hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeehhhhhhhhhhhhhhhhh......eeeee..........hhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhh.......eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yh2 D   2 PLSPILRQILQQL-----FRPDMDVKTVREQFEKSSLILVKMANEPIHRVEDITIPGRGGPIRARVYRPRDGERLPAVVYYHGGGFVLGSVETHDHVCRRLANLSGAVVVSVDYRLAPEHKFPAAVEDAYDAAKWVADNYDKLGVDNGKIAVAGDSAGGNLAAVTAIMARDRGESFVKYQVLIYPAVNLTGSPTVSRVEYSGPEYVILTADLMAWFGRQYFSKPQDALSPYASPIFADLSNLPPALVITAEYDPLRDEGELYAHLLKTRGVRAVAVRYNGVIHGFVNFYPILEEGREAVSQIAASIKSMAVA 313
                                    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  
                                       14    20                                                                                                                                                                                                                                                                                                     

   Legend:   → Mismatch (orange background)
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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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YH2)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NKS0_9CREN | Q8NKS0)
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.
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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 Related Entries

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(-) Related Entries Specified in the PDB File

2wir HYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS