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(-) Description

Title :  CRYSTAL STRUCTURE OF OPEN FORM OF MENAQUINONE-SPECIFIC ISOCHORISMATE SYNTHASE, MENF
 
Authors :  J. F. Parsons, K. M. Shi, J. E. Ladner
Date :  18 Jan 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Chorismate, Isochorismate, Menaquinone, Isomerase, Menaquinone Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. F. Parsons, K. M. Shi, J. E. Ladner
Structure Of Isochorismate Synthase In Complex With Magnesium.
Acta Crystallogr. , Sect. D V. 64 607 2008
PubMed-ID: 18453696  |  Reference-DOI: 10.1107/S0907444908005477
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MENAQUINONE-SPECIFIC ISOCHORISMATE SYNTHASE
    Chains: A
    EC Number: 5.4.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: MENF, YFBA
    Organism Scientific: ESCHERICHIA COLI
    Synonym: ISOCHORISMATE MUTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:284 , GLU A:416BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREALA A:256 , GLY A:257 , THR A:258 , GLU A:284 , ALA A:402 , GLY A:403 , GLU A:416 , LYS A:420BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREGLN A:57 , ARG A:58 , ASN A:59 , ARG A:241 , ARG A:251 , ALA A:358BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWARETYR A:368 , LEU A:386 , ARG A:387 , ALA A:400 , GLY A:401 , LYS A:420BINDING SITE FOR RESIDUE SO4 A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:50 -Pro A:51
2Trp A:166 -Pro A:167
3Gln A:340 -Pro A:341
4Leu A:348 -Pro A:349

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BZN)

(-) 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:430
 aligned with MENF_ECOLI | P38051 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:430
                                    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
           MENF_ECOLI     1 MQSLTTALENLLRHLSQEIPATPGIRVIDIPFPLKDAFDALSWLASQQTYPQFYWQQRNGDEEAVVLGAITRFTSLDQAQRFLRQHPEHADLRIWGLNAFDPSQGNLLLPRLEWRRCGGKATLRLTLFSESSLQHDAIQAKEFIATLVSIKPLPGLHLTTTREQHWPDKTGWTQLIELATKTIAEGELDKVVLARATDLHFASPVNAAAMMAASRRLNLNCYHFYMAFDGENAFLGSSPERLWRRRDKALRTEALAGTVANNPDDKQAQQLGEWLMADDKNQRENMLVVEDICQRLQADTQTLDVLPPQVLRLRKVQHLRRCIWTSLNKADDVICLHQLQPTAAVAGLPRDLARQFIARHEPFTREWYAGSAGYLSLQQSEFCVSLRSAKISGNVVRLYAGAGIVRGSDPEQEWQEIDNKAAGLRTLLQM 430
               SCOP domains d3bzna_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....eeeeeeeee......hhhhhhhhh....eeeee.....eeeeeeeeeeee.hhhhhhhhhhh........eeeee......eeeeeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.............eeeeeee.hhhhhhhhhhhhhhhhh.....eeeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee..eeeeeee..eeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...eeee...eeeeeeeeeee....hhhhhhhhhh......eehhhhhhhhhhhhh.........eeeee...eeeeee...eeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bzn A   1 MQSLTTALENLLRHLSQEIPATPGIRVIDIPFPLKDAFDALSWLASQQTYPQFYWQQRNGDEEAVVLGAITRFTSLDQAQRFLRQHPEHADLRIWGLNAFDPSQGNLLLPRLEWRRCGGKATLRLTLFSESSLQHDAIQAKEFIATLVSIKPLPGLHLTTTREQHWPDKTGWTQLIELATKTIAEGELDKVVLARATDLHFASPVNAAAMMAASRRLNLNCYHFYMAFDGENAFLGSSPERLWRRRDKALRTEALAGTVANNPDDKQAQQLGEWLMADDKNQRENMLVVEDICQRLQADTQTLDVLPPQVLRLRKVQHLRRCIWTSLNKADDVICLHQLQPTAAVAGLPRDLARQFIARHEPFTREWYAGSAGYLSLQQSEFCVSLRSAKISGNVVRLYAGAGIVRGSDPEQEWQEIDNKAAGLRTLLQM 430
                                    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
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MENF_ECOLI | P38051)
molecular function
    GO:0008909    isochorismate synthase activity    Catalysis of the reaction: chorismate = isochorismate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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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  3bzn
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 Related Entries

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

UniProtKB/Swiss-Prot
        MENF_ECOLI | P38051: 2eua 3bzm

(-) Related Entries Specified in the PDB File

3bzm