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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 :  2.80
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
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:123 , ASP A:177 , ASP A:179binding site for residue MG A 601
2AC2SOFTWAREASP B:123 , ASP B:177 , ASP B:179binding site for residue MG B 601
3AC3SOFTWAREASP C:123 , ASP C:177 , ASP C:179 , GLU C:206binding site for residue MG C 601
4AC4SOFTWAREASP D:123 , ASP D:177 , ASP D:179 , GLU D:206binding site for residue MG D 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E9F)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:329 -Ser A:330
2Ser A:330 -Ile A:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E9F)

(-) Exons   (0, 0)

(no "Exon" information available for 5E9F)

(-) 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:507
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               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.hhhhhhhhhhhhhhhhh......eeeeee......ee.....................hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhh..................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9f A   4 KNMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAEIEDEWMAKANLKRFDDAVVDVINSSSSIRNPKDVAAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVT 528
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       220       230       240       250       260       270       280       290 ||    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
                                                                                                                                                                                                                                          212|                                                                     292|                                                                                                                                                                                                                                
                                                                                                                                                                                                                                           220                                                                      304                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh.hhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhhhhh...eeeee.......eee.hhhhhhhhhhhhhhhhhhhh...eeeeee....eeee....hhhhhhhh.........hhhhhhhh.......hhhhhhh....hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhh...................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9f B   4 KNMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAEQSGKIEDEWMAKANLKRFDDAVVDVINVAAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVT 528
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       220       230       240       250       260       270       280       290     ||307       317       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527 
                                                                                                                                                                                                                                          212|                                                                         296|                   326|                                                                                                                                                                                               
                                                                                                                                                                                                                                           220                                                                          304                    337                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh........eeee......hhhhhhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhhhhhhhhhhh...eeeeeehhh.eeee....hhhhh...ee.......hhhhhhhhhh.hhhhhhhhh.eehhhhhhhhhh.hhhhhhh....hhhhhhhhhhh..................ee...hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9f C   4 KNMVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQPLADLMNTAEIEDEWMAKANLKRFDDAVVDVINAAKYLQAAKGKSNREARAIASSLGVPEIFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVT 528
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       220       230       240       250       260       270       280       290 ||    311       321    || 342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522      
                                                                                                                                                                                                                                          212|                                                                     292|                   326|                                                                                                                                                                                              
                                                                                                                                                                                                                                           220                                                                      304                    338                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh.....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhhhhhhhhhhh...eeeeeehhh.eeee....hhhhhhhh................hhhhhhhhhh................ee..hhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9f D   6 MVNPAVEPSMEDDLFAREVAEVKQWWSDPRWRYTKRPFTAEQIVSKRGNLKIEYPSNAQSKKLWKILEGRFQKRDASYTYGCLEPTMVTQMAKYLDTVYVSGWQSSSTASSSDEPGPDLADYPYTTVPNKVSHLFMAQLFHDRKQRHERLSAPKSERSKLQNIDYLRPIIADADTGHGGLTAVMKLTKLFIEKGAAGIHIEDQAPGTGKVLVPISEHINRLVAIRAQADIMGVDLLAIARTDAEAATLITTSIDPRDHAFILGCTNPSLQLKRFDGKSNREARAIASSLGFFDWDSPRTREGYFRIKGGCDCAINRAIAYAPYADAIWMESKLPDYEQAKEFAEGVHAVYPEQKLAYNLSPSFNWKTAMPRDEQETYIRRLAGLGYCWQFITLAGLHTTALISDRFARAYSEVGMRAYGELVQEPEMELGVDVVKHQKWSGATYVDELQKMVT 528
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      |222       232       242       252       262       272       282|   || 351       361|      375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525   
                                                                                                                                                                                                                                        212|                                                           282| 318|           361|                                                                                                                                                                  
                                                                                                                                                                                                                                         220                                                            314  347            366
   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 5E9F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E9F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E9F)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACEA_MAGO7 | P0CT06: 5e9g

(-) Related Entries Specified in the PDB File

5e9g 5e9h