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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MENB WITH ALTERED HEXAMERIC ASSEMBLY
 
Authors :  H-J. Li, X. Li, N. Liu, H. Zhang, J. Truglio, S. Mishra, C. Kisker, M. Garc P. Tonge
Date :  01 Aug 11  (Deposition) - 24 Aug 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Crotonase Superfamily, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Li, X. Li, N. Liu, H. Zhang, J. J. Truglio, S. Mishra, C. Kisker, M. Garcia-Diaz, P. J. Tonge
Mechanism Of The Intramolecular Claisen Condensation Reaction Catalyzed By Menb, A Crotonase Superfamily Member.
Biochemistry V. 50 9532 2011
PubMed-ID: 21830810  |  Reference-DOI: 10.1021/BI200877X

(-) Compounds

Molecule 1 - 1,4-DIHYDROXY-2-NAPHTHOYL-COA SYNTHASE
    Chains: A, B
    EC Number: 4.1.3.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV0548C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: MENB, DHNA-COA SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:83 , PRO A:147 , LYS A:148 , VAL A:149 , PRO A:255 , ARG A:259 , HOH A:333 , HOH A:387BINDING SITE FOR RESIDUE GOL A 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T8B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:91 -Pro A:92
2Gly B:91 -Pro B:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T8B)

(-) Exons   (0, 0)

(no "Exon" information available for 3T8B)

(-) 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:237
 aligned with MENB_MYCTO | P9WNP4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:258
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
           MENB_MYCTO    16 SDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLV 273
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..........eee.........---------------------..hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.............hhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhh...eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t8b A  16 SDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRG---------------------RLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLV 273
                                    25        35        45        55        65        75        85        95       105     |   -         -       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
                                                                                                                         111                   133                                                                                                                                            


Chain A from PDB  Type:PROTEIN  Length:237
 aligned with MENB_MYCTU | P9WNP5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:258
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
           MENB_MYCTU    16 SDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLV 273
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..........eee.........---------------------..hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee.............hhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhh...eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t8b A  16 SDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRG---------------------RLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLV 273
                                    25        35        45        55        65        75        85        95       105     |   -         -       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
                                                                                                                         111                   133                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with MENB_MYCTO | P9WNP4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:238
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246        
           MENB_MYCTO    17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKS 254
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee.....------------------------...hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee...----------.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t8b B  17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQ------------------------GRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTD----------GSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKS 254
                                    26        36        46        56        66        76        86        96       106|        -         -     | 136       146       156       166       176        |-       196       206       216       226       236       246        
                                                                                                                    107                      132                                                  185        196                                                          


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with MENB_MYCTU | P9WNP5 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:238
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246        
           MENB_MYCTU    17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKS 254
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee.........eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..........eee.....------------------------...hhhhhhhhhhhh..eeeeee..eeehhhhhhhhhh.eeeee....eee...----------.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t8b B  17 DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQ------------------------GRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTD----------GSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKS 254
                                    26        36        46        56        66        76        86        96       106|        -         -     | 136       146       156       166       176        |-       196       206       216       226       236       246        
                                                                                                                    107                      132                                                  185        196
   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 3T8B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T8B)

(-) Gene Ontology  (7, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MENB_MYCTO | P9WNP4)
molecular function
    GO:0008935    1,4-dihydroxy-2-naphthoyl-CoA synthase activity    Catalysis of the reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-napthoyl-CoA + H2O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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.
    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.

Chain A,B   (MENB_MYCTU | P9WNP5)
molecular function
    GO:0008935    1,4-dihydroxy-2-naphthoyl-CoA synthase activity    Catalysis of the reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-napthoyl-CoA + H2O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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.
    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.
    GO:0034214    protein hexamerization    The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits.
cellular component
    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.

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  3t8b
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  MENB_MYCTU | P9WNP5
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  4.1.3.36
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 Related Entries

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

UniProtKB/Swiss-Prot
        MENB_MYCTO | P9WNP4: 1q51 1q52 1rjm 1rjn 3t8a
        MENB_MYCTU | P9WNP5: 1q51 1q52 1rjm 1rjn 3t8a 4qii 4qij

(-) Related Entries Specified in the PDB File

3t88 CRYSTAL STRUCTURE OF ESCHERICHIA COLI MENB IN COMPLEX WITH SUBSTRATE ANALOGUE, OSB-NCOA
3t89 CRYSTAL STRUCTURE OF ESCHERICHIA COLI MENB
3t8a CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MENB IN COMPLEX WITH SUBSTRATE ANALOGUE, OSB-NCOA