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(-) Description

Title :  STRUCTURAL INSIGHTS OF ISOCITRATE LYASES FROM MAGNAPORTHE ORYZAE
 
Authors :  Y. Park, Y. Cho, Y. -H. Lee, Y. -W. Lee, S. Rhee
Date :  15 Oct 15  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Beta/Alpha-Barrel, Lyase Activity, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Park, Y. Cho, Y. -H. Lee, Y. -W. Lee, S. Rhee
Crystal Structure And Functional Analysis Of Isocitrate Lyases From Magnaporthe Oryzae And Fusarium Graminearum
J. Struct. Biol. V. 194 395 2016
PubMed-ID: 27016285  |  Reference-DOI: 10.1016/J.JSB.2016.03.019

(-) Compounds

Molecule 1 - ISOCITRATE LYASE
    Chains: A, B, C, D
    EC Number: 4.1.3.1, 4.1.3.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ICL1, MGG_04895
    Mutation: YES
    Organism Common: RICE BLAST FUNGUS
    Organism Scientific: MAGNAPORTHE ORYZAE 70-15
    Organism Taxid: 242507
    Strain: 70-15
    Synonym: ICL,ISOCITRASE,ISOCITRATASE,METHYLISOCITRATE LYASE,MICA, THREO-D(S)-ISOCITRATE GLYOXYLATE-LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GLV4Ligand/IonGLYOXYLIC ACID
2GOL3Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:104 , SER A:106 , GLY A:107 , TRP A:108 , ASP A:177 , HIS A:204 , ARG A:252 , TRP A:403 , THR A:467 , MG A:603binding site for residue GLV A 601
02AC2SOFTWARETRP A:108 , CYS A:215 , GLY A:216 , HIS A:217 , ARG A:252 , GLU A:405 , ASN A:433 , SER A:435 , THR A:467 , HOH A:716binding site for residue GOL A 602
03AC3SOFTWAREASP A:177 , GLV A:601 , HOH A:701 , HOH A:716 , HOH A:717binding site for residue MG A 603
04AC4SOFTWARETYR B:104 , SER B:106 , GLY B:107 , TRP B:108 , ASP B:177 , HIS B:204 , ARG B:252 , TRP B:403 , THR B:467 , GOL B:602 , MG B:603binding site for residue GLV B 601
05AC5SOFTWARECYS B:215 , GLY B:216 , HIS B:217 , ARG B:252 , GLU B:405 , ASN B:433 , SER B:435 , SER B:437 , THR B:467 , GLV B:601 , HOH B:704binding site for residue GOL B 602
06AC6SOFTWAREASP B:177 , LYS B:213 , GLV B:601 , HOH B:702 , HOH B:704 , HOH B:705binding site for residue MG B 603
07AC7SOFTWARETYR C:104 , SER C:106 , GLY C:107 , TRP C:108 , ASP C:177 , ARG C:252 , TRP C:403 , MG C:602 , HOH C:706 , HOH C:723 , HOH C:728binding site for residue GLV C 601
08AC8SOFTWAREASP C:177 , GLV C:601 , HOH C:706 , HOH C:707 , HOH C:726binding site for residue MG C 602
09AC9SOFTWARETYR D:104 , SER D:106 , GLY D:107 , TRP D:108 , ASP D:177 , HIS D:204 , ARG D:252 , TRP D:403 , THR D:467 , GOL D:602 , MG D:603binding site for residue GLV D 601
10AD1SOFTWARECYS D:215 , GLY D:216 , HIS D:217 , ARG D:252 , GLU D:405 , ASN D:433 , SER D:435 , SER D:437 , GLV D:601 , HOH D:703binding site for residue GOL D 602
11AD2SOFTWAREASP D:177 , GLV D:601 , HOH D:703 , HOH D:709 , HOH D:710binding site for residue MG D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E9G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E9G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E9G)

(-) Exons   (0, 0)

(no "Exon" information available for 5E9G)

(-) 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:524
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhhhhhh..eeeee...............ee.hhhhhhhhhhhhhhhhhhhh...eeeeee......ee....hhhhh............hhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhh..................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9g A   5 NMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTKKCGHMGGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAEQSGKTGDQLQAIEDEWMAKANLKRFDDAVVDVINSSSSIRNPKDVAAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVT 528
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524    


Chain B from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhhhhhh..eeeee...............ee.hhhhhhhhhhhhhhhhhhh....eeeeee......ee....hhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhh..................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9g B   5 NMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTKKCGHMGGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAEQSGKTGDQLQAIEDEWMAKANLKRFDDAVVDVINSSSSIRNPKDVAAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVTG 529
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524     


Chain C from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhhh..eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhhh...eeeeee......ee....hhhhh............hhhhhhhh..hhhhhhhhh..hhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9g C   5 NMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTKKCGHMGGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAIEDEWMAKANLKRFDDAVVDVINAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMV 527
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      |306       316       326|      348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518         
                                                                                                                                                                                                                                                                                                                        291|                   326|                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                         304                    339                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhhhhhh..eeeee...............ee.hhhhhhhhhhhhhhhhhhhh...eeeeee......ee....hhhhhh...........hhhhhh..hhhhhh...hhhhhh...hhhhhh..hhhhhhhhhhh.............ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee..........hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e9g D   5 NMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTKKCGHMGGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNEWMAKANLKRFDDAVVDAKYLQAAKGKSNREARAIASSFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVTG 529
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    || 311       321 ||    346       356  ||   372       382       392       402       412       422       432       443       453       463       473       483       493       503       513       523      
                                                                                                                                                                                                                                                                                                                      289|             323|                 359|                                                                        441|                                                                                      
                                                                                                                                                                                                                                                                                                                       307              339                  366                                                                         443
   Legend:   → Mismatch (orange background)
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  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 5E9G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E9G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E9G)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  5e9g
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        ACEA_MAGO7 | P0CT06: 5e9f

(-) Related Entries Specified in the PDB File

5e9f 5e9h