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(-) Description

Title :  CRYSTAL STRUCTURE OF TT0310 PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. Kunishima, M. Sugahara, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Jun 04  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Thioesterase, Hot Dog Fold, Phenylacetic Acid Degradation, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kunishima, Y. Asada, M. Sugahara, J. Ishijima, Y. Nodake, M. Sugahara, M. Miyano, S. Kuramitsu, S. Yokoyama, M. Sugahara
A Novel Induced-Fit Reaction Mechanism Of Asymmetric Hot Dog Thioesterase Paai
J. Mol. Biol. V. 352 212 2005
PubMed-ID: 16061252  |  Reference-DOI: 10.1016/J.JMB.2005.07.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHENYLACETIC ACID DEGRADATION PROTEIN PAAI
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS HB8
    Organism Taxid300852
    StrainHB8 / ATCC 27634 / DSM 579
    SynonymPAAI PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)ABCD    
Biological Unit 2 (1x)    EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3COA4Ligand/IonCOENZYME A
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3COA2Ligand/IonCOENZYME A
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3COA2Ligand/IonCOENZYME A

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:67 , ARG B:67 , ARG C:67 , ARG D:67BINDING SITE FOR RESIDUE CL A 2001
2AC2SOFTWAREARG E:67 , ARG F:67 , ARG G:67 , ARG H:67BINDING SITE FOR RESIDUE CL H 2002
3AC3SOFTWAREPRO B:60 , ALA E:8 , LEU E:9 , ARG E:28 , ASP E:30 , HIS E:31 , ALA G:8BINDING SITE FOR RESIDUE ACT E 2007
4AC4SOFTWAREALA A:63 , LEU A:64 , PHE A:115 , ASN C:33 , ALA C:38 , TYR C:70 , PHE C:71 , ARG C:72 , PRO C:73 , LYS C:105 , HOH C:2024 , HOH C:2025 , HOH C:2027 , HOH C:2047 , HOH C:2077 , HOH C:2085 , SER D:90 , ARG D:91 , ARG D:92 , HOH D:149 , GLY H:10 , HOH H:2022 , HOH H:2056BINDING SITE FOR RESIDUE COA C 2003
5AC5SOFTWAREVAL B:62 , ALA B:63 , LEU B:64 , SER C:90 , ARG C:91 , ARG C:92 , HOH C:2029 , HOH C:2030 , HOH C:2032 , TYR D:70 , PHE D:71 , PRO D:73BINDING SITE FOR RESIDUE COA C 2004
6AC6SOFTWAREHIS A:35 , GLY A:36 , ALA E:63 , PHE E:115 , LEU E:117 , ASN G:33 , TYR G:70 , PHE G:71 , PRO G:73 , HOH G:2022 , SER H:90 , ARG H:91 , ARG H:92 , HOH H:2028 , HOH H:2029 , HOH H:2031 , HOH H:2032 , HOH H:2033BINDING SITE FOR RESIDUE COA H 2005
7AC7SOFTWAREHIS B:35 , GLY B:36 , HOH B:143 , ALA F:63 , PHE F:115 , SER G:90 , ARG G:91 , ARG G:92 , HOH G:2023 , HOH G:2026 , HOH G:2028 , HOH G:2086 , ASN H:33 , TYR H:70 , PHE H:71 , PRO H:73 , HOH H:2038BINDING SITE FOR RESIDUE COA G 2006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WLV)

(-) Exons   (0, 0)

(no "Exon" information available for 1WLV)

(-) 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:117
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
         Q5SJP3_THET8     1 MRDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlva_ A: automated matches                                                                                          SCOP domains
               CATH domains 1wlvA00 A:1-117  [code=3.10.129.10, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv A   1 MRDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    10        20        30        40        50        60        70        80        90       100       110       

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
         Q5SJP3_THET8     2 RDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvb_ B: automated matches                                                                                         SCOP domains
               CATH domains 1wlvB00 B:2-117  [code=3.10.129.10, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv B   2 RDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    11        21        31        41        51        61        71        81        91       101       111      

Chain C from PDB  Type:PROTEIN  Length:115
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q5SJP3_THET8     3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvc_ C: automated matches                                                                                        SCOP domains
               CATH domains 1wlvC00 C:3-117  [code=3.10.129.10, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv C   3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    12        22        32        42        52        62        72        82        92       102       112     

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q5SJP3_THET8     3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvd_ D: automated matches                                                                                        SCOP domains
               CATH domains 1wlvD00 D:3-117  [code=3.10.129.10, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv D   3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    12        22        32        42        52        62        72        82        92       102       112     

Chain E from PDB  Type:PROTEIN  Length:115
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q5SJP3_THET8     3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlve_ E: automated matches                                                                                        SCOP domains
               CATH domains 1wlvE00 E:3-117  [code=3.10.129.10, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv E   3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    12        22        32        42        52        62        72        82        92       102       112     

Chain F from PDB  Type:PROTEIN  Length:115
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q5SJP3_THET8     3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvf_ F: automated matches                                                                                        SCOP domains
               CATH domains 1wlvF00 F:3-117  [code=3.10.129.10, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv F   3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    12        22        32        42        52        62        72        82        92       102       112     

Chain G from PDB  Type:PROTEIN  Length:115
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q5SJP3_THET8     3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvg_ G: automated matches                                                                                        SCOP domains
               CATH domains 1wlvG00 G:3-117  [code=3.10.129.10, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv G   3 DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    12        22        32        42        52        62        72        82        92       102       112     

Chain H from PDB  Type:PROTEIN  Length:117
 aligned with Q5SJP3_THET8 | Q5SJP3 from UniProtKB/TrEMBL  Length:136

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
         Q5SJP3_THET8     1 MRDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
               SCOP domains d1wlvh_ H: automated matches                                                                                          SCOP domains
               CATH domains 1wlvH00 H:1-117  [code=3.10.129.10, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlv H   1 MRDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFRL 117
                                    10        20        30        40        50        60        70        80        90       100       110       

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WLV)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (Q5SJP3_THET8 | Q5SJP3)
molecular function
    GO:0016790    thiolester hydrolase activity    Catalysis of the reaction: RCO-SR' + H2O = RCOOH + HSR'. This reaction is the hydrolysis of a thiolester bond, an ester formed from a carboxylic acid and a thiol (i.e., RCO-SR'), such as that found in acetyl-coenzyme A.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5SJP3_THET8 | Q5SJP31j1y 1wlu 1wm6 1wn3 2dsl

(-) Related Entries Specified in the PDB File

1wlu UNLIGANDED FORM IN SPACE GROUP I4122 RELATED ID: TTK003000310.4 RELATED DB: TARGETDB