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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E190A MUTANT OF O-SUCCINYLBENZOATE SYNTHASE FROM ESCHERICHIA COLI
 
Authors :  R. A. Nagatani, A. Gonzalez, B. K. Shoichet, L. S. Brinen, P. C. Babbitt
Date :  03 Jan 07  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Nagatani, A. Gonzalez, B. K. Shoichet, L. S. Brinen, P. C. Babbitt
Stability For Function Trade-Offs In The Enolase Superfamil "Catalytic Module".
Biochemistry V. 46 6688 2007
PubMed-ID: 17503785  |  Reference-DOI: 10.1021/BI700507D

(-) Compounds

Molecule 1 - O-SUCCINYLBENZOATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MENC, B2261, JW2256
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI STR. K-12 SUBSTR.
    Organism Taxid: 511145
    Strain: MG1655
    Synonym: OSB SYNTHASE, OSBS, 4-(2'-CARBOXYPHENYL)-4-OXYBUTYRIC ACID SYNTHASE, O-SUCCINYLBENZOIC ACID SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OFJ)

(-) Sites  (0, 0)

(no "Site" information available for 2OFJ)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:75 -C:75
2B:75 -D:75

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OFJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OFJ)

(-) 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:300
 aligned with MENC_ECOLI | P29208 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       320
           MENC_ECOLI     1 MRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCNGDPDDLILKLADMPGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLEEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
               SCOP domains d2ofja2 A:1-99        O-succinylbenzoate synthase                                                  d2ofja1 A:10             0-320 O-succinylbenzoate synthase                                                                                                                                                                    SCOP domains
               CATH domains 2ofjA01 A:1-96       ,A:295-320 Enolase-like, N-terminal domain                                 2ofjA02 A:97-29             4 Enolase superfamily                                                                                                                                                     2ofjA01 A:1-96,A:295-320   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..-------....eeeeeeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.............ee.-------------...eeeeee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh.....hhh.eeeee....hhhhhhhhhhhhh..eee................eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh........hhhhh..ee..........eehhhhheeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofj A   1 MRSAQVYRWQIPMD-------RRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCN-------------PGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLAEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
                                    10   |     - |      30        40        50        60        70        80        90       100       110|        -    |  130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
                                        14      22                                                                                      111           125                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with MENC_ECOLI | P29208 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       320
           MENC_ECOLI     1 MRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCNGDPDDLILKLADMPGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLEEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
               SCOP domains d2ofjb2 B:1-99        O-succinylbenzoate synthase                                                  d2ofjb1 B:10             0-320 O-succinylbenzoate synthase                                                                                                                                                                    SCOP domains
               CATH domains 2ofjB01 B:1-96       ,B:295-320 Enolase-like, N-terminal domain                                 2ofjB02 B:97-29             4 Enolase superfamily                                                                                                                                                     2ofjB01 B:1-96,B:295-320   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..-------....eeeeeeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh................-------------...eeeeee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh.....hhh.eeeee....hhhhhhhhhhhhh..eeehhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh........hhhhh..ee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofj B   1 MRSAQVYRWQIPMD-------RRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCN-------------PGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLAEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
                                    10   |     - |      30        40        50        60        70        80        90       100       110|        -    |  130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
                                        14      22                                                                                      111           125                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:296
 aligned with MENC_ECOLI | P29208 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       320
           MENC_ECOLI     1 MRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCNGDPDDLILKLADMPGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLEEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
               SCOP domains d2ofjc2 C:1-99          O-succinylbenzoate synthase                                                d2ofjc1 C:10               0-320 O-succinylbenzoate synthase                                                                                                                                                                  SCOP domains
               CATH domains 2ofjC01 C:1-96         ,C:295-320 Enolase-like, N-terminal domain                               2ofjC02 C:97-29               4 Enolase superfamily                                                                                                                                                   2ofjC01 C:1-96,C:295-320   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..---------..eeeeeeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh................---------------.eeeeee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhhhhh..eee................eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...............ee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofj C   1 MRSAQVYRWQIPMD---------LKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCN---------------EKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLAEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
                                    10   |     -   |    30        40        50        60        70        80        90       100       110|        -      |130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
                                        14        24                                                                                    111             127                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with MENC_ECOLI | P29208 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:320
                                    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       320
           MENC_ECOLI     1 MRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCNGDPDDLILKLADMPGEKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLEEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
               SCOP domains d2ofjd2 D:1-9          9 O-succinylbenzoate synthase                                               d2ofjd1 D:100-3            20 O-succinylbenzoate synthase                                                                                                                                                                     SCOP domains
               CATH domains 2ofjD01 D:1-9          6,D:295-320 Enolase-like, N-terminal domain                              2ofjD02 D:97-294 E            nolase superfamily                                                                                                                                                      2ofjD01 D:1-96,D:295-320   CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-2ofjD01 D:145-213                                             ----------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-2ofjD02 D:145-213                                             ----------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-2ofjD03 D:145-213                                             ----------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-2ofjD04 D:145-213                                             ----------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeeeeeee.----------..eeeeeeeeeee..eeeeee..........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...................------------..eeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhhhhh..eeehhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh........hhhhh..ee..........eehhhhheeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofj D   1 MRSAQVYRWQIPM----------LKTRDGLYVCLREGEREGWGEISPLPGFSQETWEEAQSVLLAWVNNWLAGDCELPQMPSVAFGVSCALAELTDTLPQAANYRAAPLCNGDP------------EKVAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKGQQFAKYVNPDYRDRIAFLAEPCKTRDDSRAFARETGIAIAWDESLREPDFAFVAEEGVRAVVIKPTLTGSLEKVREQVQAAHALGLTAVISSSIESSLGLTQLARIAAWLTPDTIPGLDTLDLMQAQQVRRWPGSTLPVVEVDALERLL 320
                                    10  |      -   |    30        40        50        60        70        80        90       100       110   |     -      |130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
                                       13         24                                                                                       114          127
   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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MENC_ECOLI | P29208)
molecular function
    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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    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.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MENC_ECOLI | P29208: 1fhu 1fhv 1r6w

(-) Related Entries Specified in the PDB File

1fhu THE APO STRUCTURE OF THE WILD-TYPE PROTEIN
1fhv THE WILD-TYPE PROTEIN COMPLEX WITH OSB