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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE
 
Authors :  Structural Genomix, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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 :  Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YDII
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YDII, B1686
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VI8)

(-) Sites  (0, 0)

(no "Site" information available for 1VI8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI8)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI8)

(-) 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:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8a_ A: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8A00 A:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh.hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 A   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129        


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:146
                             1                                                                                                                                    136         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      |  -      
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL---------   -
               SCOP domains d1vi8b_ B: Hypothetical protein YdiI                                                                                                               SCOP domains
               CATH domains 1vi8B00 B:0-145  [code=3.10.129.10, no name defined]                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi8 B   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILEGGSHHHHH 145
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139      


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8c_ C: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8C00 C:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhh....hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 C   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129        


Chain D from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8d_ D: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8D00 D:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh....hhhhh.eeeee....eeeee.............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee........eeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 D   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129        


Chain E from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8e_ E: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8E00 E:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 E   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129        


Chain F from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8f_ F: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8F00 F:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh...hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 F   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129        


Chain G from PDB  Type:PROTEIN  Length:137
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:137
                                                                                                                                                                 136 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     | 
           MENI_ECOLI     1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8g_ G: Hypothetical protein YdiI                                                                                                      SCOP domains
               CATH domains 1vi8G00 G:1-137  [code=3.10.129.10, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi8 G   1 LIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain H from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                             1                                                                                                                                    136 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      | 
           MENI_ECOLI     - -MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL-   -
               SCOP domains d1vi8h_ H: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains 1vi8H00 H:0-137  [code=3.10.129.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi8 H   0 SLIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILE 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VI8)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (MENI_ECOLI | P77781)
molecular function
    GO:0061522    1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity    Catalysis of the reaction 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA.
    GO:0016289    CoA hydrolase activity    Catalysis of the reaction: X-CoA + H2O = X + CoA; X may be any group.
    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: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.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

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  1vi8
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  MENI_ECOLI | P77781
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 Related Entries

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

UniProtKB/Swiss-Prot
        MENI_ECOLI | P77781: 1sbk 1vh5 4k49 4k4a 4k4b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VI8)