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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HSAD FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  N. Lack, E. D. Lowe, J. Liu, L. D. Eltis, M. E. M. Noble, E. Sim, I. M. Westwood
Date :  29 Oct 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Meta-Cleavage Product Hydrolase, Hsad, Hydrolase, Serine Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Lack, E. D. Lowe, J. Liu, L. D. Eltis, M. E. M. Noble, E. Sim, I. M. Westwood
Structure Of Hsad, A Steroid-Degrading Hydrolase, From Mycobacterium Tuberculosis.
Acta Crystallogr. , Sect. F V. 64 2 2008
PubMed-ID: 18097091  |  Reference-DOI: 10.1107/S1744309107065931

(-) Compounds

Molecule 1 - 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
    Chains: A, B
    EC Number: 3.7.1.8
    Engineered: YES
    Expression System: PSEUDOMONAS PUTIDA
    Expression System Plasmid: PVLT31
    Expression System Strain: KT4224
    Expression System Taxid: 303
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: 2,6-DIOXO-6-PHENYLHEXA-3-ENOATE HYDROLASE, 2-HYDROXY-6-PHENYLHEXA-2,4-DIENOIC ACID HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:143 , ILE B:144 , ASN B:145 , ASP B:150BINDING SITE FOR RESIDUE GOL B1291
2AC2SOFTWARETHR A:53 , SER A:56 , PRO A:186 , GLU A:187BINDING SITE FOR RESIDUE GOL A1291
3AC3SOFTWAREASP B:21 , HIS B:85 , GLY B:86 , TYR B:91 , MET B:94 , HOH B:2077 , HOH B:2078BINDING SITE FOR RESIDUE GOL B1292
4AC4SOFTWAREARG A:157 , ARG A:175 , LYS A:181 , HOH A:2126 , LYS B:156BINDING SITE FOR RESIDUE SO4 A1292
5AC5SOFTWARELYS A:156 , ARG B:157 , LYS B:181BINDING SITE FOR RESIDUE SO4 B1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VF2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:150 -Pro A:151
2Asp B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VF2)

(-) Exons   (0, 0)

(no "Exon" information available for 2VF2)

(-) 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:284
 aligned with HSAD_MYCTO | P9WNH4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           HSAD_MYCTO     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
               SCOP domains d2vf2a_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeeeeeeee......eeeee.......hhhhhh..hhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf2 A   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    


Chain A from PDB  Type:PROTEIN  Length:284
 aligned with HSAD_MYCTU | P9WNH5 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           HSAD_MYCTU     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
               SCOP domains d2vf2a_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeeeeeeee......eeeee.......hhhhhh..hhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf2 A   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with HSAD_MYCTO | P9WNH4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           HSAD_MYCTO     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
               SCOP domains d2vf2b_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------Abhydrolase_6-2vf2B01 B:39-282                                                                                                                                                                                                                      -------- Pfam domains (1)
           Pfam domains (2) --------------------------------Abhydrolase_6-2vf2B02 B:39-282                                                                                                                                                                                                                      -------- Pfam domains (2)
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhh..hhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf2 B   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with HSAD_MYCTU | P9WNH5 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           HSAD_MYCTU     7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
               SCOP domains d2vf2b_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------Abhydrolase_6-2vf2B01 B:39-282                                                                                                                                                                                                                      -------- Pfam domains (1)
           Pfam domains (2) --------------------------------Abhydrolase_6-2vf2B02 B:39-282                                                                                                                                                                                                                      -------- Pfam domains (2)
         Sec.struct. author .hhhhheeeeee.....eeeeeeee......eeeee.......hhhhhh..hhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf2 B   7 LTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGG 290
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VF2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (11, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HSAD_MYCTU | P9WNH5)
molecular function
    GO:0018774    2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity    Catalysis of the reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.
    GO:0034820    4,9-DSHA hydrolase activity    Catalysis of the reaction: (3E,1Z)-4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate + H2O = (2E,4E)-2-hydroxyhexa-2,4-dienoate + 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate + H+.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0044117    growth of symbiont in host    The increase in size or mass of an organism, occurring within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (HSAD_MYCTO | P9WNH4)
molecular function
    GO:0018774    2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity    Catalysis of the reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.
    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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.

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  2vf2
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  HSAD_MYCTO | P9WNH4
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  HSAD_MYCTU | P9WNH5
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  3.7.1.8
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  HSAD_MYCTO | P9WNH4
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 Related Entries

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

UniProtKB/Swiss-Prot
        HSAD_MYCTO | P9WNH4: 2wud 2wue 2wuf 2wug 5jz9
        HSAD_MYCTU | P9WNH5: 2wud 2wue 2wuf 2wug 5jzb 5jzs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VF2)