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(-) Description

Title :  CRYSTAL STRUCTURE OF MEND FROM E.COLI
 
Authors :  A. Priyadarshi, K. Y. Hwang
Date :  19 Dec 08  (Deposition) - 24 Mar 09  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Menaquinone Biosynthesis Protein, Magnesium, Manganese, Menaquinone Biosynthesis, Metal-Binding, Thiamine Pyrophosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Priyadarshi, Y. Saleem, K. H. Nam, K. S. Kim, S. Y. Park, E. E. Kim, K. Y. Hwang
Structural Insights Of The Mend From Escherichia Coli Revea Thdp Affinity.
Biochem. Biophys. Res. Commun. V. 380 797 2009
PubMed-ID: 19338755  |  Reference-DOI: 10.1016/J.BBRC.2009.01.168

(-) Compounds

Molecule 1 - 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1- CARBOXYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.2.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2264, JW5374, MEND
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: SEPHCHC SYNTHASE, MENAQUINONE BIOSYNTHESIS PROTEIN MEND

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3FLM)

(-) Sites  (0, 0)

(no "Site" information available for 3FLM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:172 -Pro A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FLM)

(-) Sequences/Alignments

Asymmetric/Biological 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:535
 aligned with MEND_ECOLI | P17109 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
           MEND_ECOLI     2 SVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVSTIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWLREAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQVSHL 556
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...................eeee........hhhhhhhhhhhhhhh.....eeeeee.....---....hhhhhhhhhhhhhh.................hhhhhh...eeeee...hhhhhhhhhhhhhhhh..eee.hhhh......hhhhhh.hhhhhhhhh...eeeee.....hhhhhhhhhhh...eeeeee............eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhh.hhhhhhhh....eeeeeee...-----------------........hhhhhhhh..eee...hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flm A   2 SVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTLLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVSTIDHALGTLHAGGVHINCPFAEPL---MDDTGLSWQQRLGDWWQDDKPWLREAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNNG-----------------YLMPQNVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQVSHL 556
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171  |   |181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471         -       491       501       511       521       531       541       551     
                                                                                                                                                                                                      174 178                                                                                                                                                                                                                                                                                                  471               489                                                                   


Chain B from PDB  Type:PROTEIN  Length:531
 aligned with MEND_ECOLI | P17109 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:556
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550      
           MEND_ECOLI     1 MSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVSTIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWLREAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQVSHL 556
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...................eeee........hhhhhhhhhhhhhhh.....eeeeee.....--.....hhhhhhhhhhhhhh.................hhhhhh...eeeee...hhhhhhhhhhhhhhhh..eee...........hhhhhh.hhhhhhhhh...eeeee.....hhhhhhhhhhh...eeeeee............eeeee.hhhhhhhhh..........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.......ee.........hhhhhhhhhhhhhh..eeeeeehhhhhhh..hhhhhh.....eeeeeee..-----------------------...hhhhhhhhh.eee...hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flm B   1 MSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTLLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVSTIDHALGTLHAGGVHINCPFAEPL--EMDDTGLSWQQRLGDWWQDDKPWLREAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNN-----------------------NVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQVSHL 556
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         -         -   |   500       510       520       530       540       550      
                                                                                                                                                                                                       174  |                                                                                                                                                                                                                                                                                                  470                     494                                                              
                                                                                                                                                                                                          177
   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 3FLM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MEND_ECOLI | P17109)
molecular function
    GO:0070204    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity    Catalysis of the reaction: 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2).
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

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  Cis Peptide Bonds
    Glu A:172 - Pro A:173   [ RasMol ]  
 

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  2.2.1.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        MEND_ECOLI | P17109: 2jla 2jlc 3hww 3hwx 5ej4 5ej5 5ej6 5ej7 5ej8 5ej9 5eja 5ejm

(-) Related Entries Specified in the PDB File

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