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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI MENH
 
Authors :  J. M. Johnston, E. N. Baker, Z. Guo, M. Jiang
Date :  31 Jul 12  (Deposition) - 08 May 13  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Menaquinone Biosynthesis, Alpha Beta Hydrolase, 2-Succinyl-6-Hydroxy- 2, 4-Cyclohexadiene-1-Carboxylate Synthase, Menh, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Johnston, M. Jiang, Z. Guo, E. N. Baker
Crystal Structures Of E. Coli Native Menh And Two Active Site Mutants.
Plos One V. 8 61325 2013
PubMed-ID: 23637813  |  Reference-DOI: 10.1371/JOURNAL.PONE.0061325

(-) Compounds

Molecule 1 - 2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE
    Chains: A, B, C
    EC Number: 4.2.99.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B2263, JW2258, MENH, YFBB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: SHCHC SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:86 , LEU A:87 , ARG A:90 , ARG A:124 , HOH A:409 , HOH A:427BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARETYR A:85 , TYR A:148 , ARG A:168 , ASN A:233BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWARESER B:86 , LEU B:87 , ARG B:90 , ARG B:124 , HOH B:401 , HOH B:416BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWARELYS B:8 , HIS B:9 , PRO C:15 , TRP C:81 , CYS C:104BINDING SITE FOR RESIDUE SO4 B 302
5AC5SOFTWARETYR B:85 , TYR B:148 , ARG B:168 , ASN B:233 , HOH B:417BINDING SITE FOR RESIDUE CL B 303
6AC6SOFTWAREHIS A:9 , ARG B:198 , ALA B:201 , PHE B:202BINDING SITE FOR RESIDUE GOL B 304
7AC7SOFTWARESER C:86 , LEU C:87 , ARG C:90 , ARG C:124 , HOH C:409 , HOH C:410BINDING SITE FOR RESIDUE SO4 C 301
8AC8SOFTWARETYR C:85 , TYR C:148 , ARG C:168 , ASN C:233BINDING SITE FOR RESIDUE CL C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GDM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GDM)

(-) Exons   (0, 0)

(no "Exon" information available for 4GDM)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......eeeee.........hhhhhh.....eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhh...eeeeeee..hhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gdm A   0 SMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee.......eeeee.........hhhhhhhhh..eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhh...eeeeeee..hhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gdm B  -5 LVPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244        


Chain C from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.......eeeee.........hhhhhh.....eeeee....hhhhh.....hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee..hhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gdm C  -6 GLVPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243
   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 4GDM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GDM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GDM)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  4gdm
    Family and Domain Information: ProDom | SYSTERS
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Access by UniProt ID/Accession number
  MENH_ECOLI | P37355
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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  4.2.99.20
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  MENH_ECOLI | P37355
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 Related Entries

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

UniProtKB/Swiss-Prot
        MENH_ECOLI | P37355: 4gec 4geg 4mxd 4myd 4mys

(-) Related Entries Specified in the PDB File

4gec E. COLI MENH R124A MUTANT STRUCTURE
4geg E. COLI MENH Y85F MUTANT STRUCTURE