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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI MENH R124A MUTANT
 
Authors :  J. M. Johnston, E. N. Baker, Z. Guo, M. Jiang
Date :  01 Aug 12  (Deposition) - 08 May 13  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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, Mutant R124A, Menh Mutant R124A, 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, MENH_R124AMUTANT, YFBB
    Mutation: YES
    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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:8 , HIS A:9 , PRO C:15 , TRP C:81 , CYS C:104BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARESER A:86 , LEU A:87 , ARG A:90 , HOH A:401 , HOH A:408 , HOH A:451BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG A:198 , PHE A:200 , ALA A:201 , PHE A:202 , HOH A:422 , HIS B:9BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWARETYR A:85 , TYR A:148 , ARG A:168 , ASN A:233 , HOH A:434 , HOH A:493BINDING SITE FOR RESIDUE CL A 304
5AC5SOFTWAREALA A:36 , ALA A:247 , ARG A:251 , ALA B:36 , PHE B:37 , ALA B:247 , ARG B:251BINDING SITE FOR RESIDUE EDO A 305
6AC6SOFTWARESER B:86 , LEU B:87 , ARG B:90 , HOH B:437 , HOH B:446 , HOH B:449BINDING SITE FOR RESIDUE SO4 B 301
7AC7SOFTWARETYR B:85 , TYR B:148 , ARG B:168 , ASN B:233BINDING SITE FOR RESIDUE CL B 302
8AC8SOFTWARESER C:86 , LEU C:87 , ARG C:90 , HOH C:401BINDING SITE FOR RESIDUE SO4 C 301
9AC9SOFTWARETYR 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 4GEC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly C:-6 -Leu C:-5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEC)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......eeeee.........hhhhhhhhh..eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhh...eeeeeee..hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gec A  -4 VPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAEAQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       


Chain B 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.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhh...eeeeeee..hhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gec B   0 SMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAEAQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 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 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.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gec C  -6 GLVPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGYSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAEAQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 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 4GEC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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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: 4gdm 4geg 4mxd 4myd 4mys

(-) Related Entries Specified in the PDB File

4gdm NATIVE E. COLI MENH STRUCTURE
4geg E. COLI MENH Y85F MUTANT STRUCTURE