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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-VINYL GLYOXYLATE MODIFIED ISOCITRATE LYASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  H. -L. Huang, T. D. Meek
Date :  14 Sep 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Sharma, S. Sharma, K. Hoener Zu Bentrup, J. D. Mckinney, D. G. Russell, W. R. Jacobs, J. C. Sacchettini
Crystal Structure Of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOCITRATE LYASE 1
    Chains: A, B, C, D
    EC Number: 4.1.3.1, 4.1.3.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30(B)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: ICL1, ERDMAN_0512, Q643_00485
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 35801 / TMC 107 / ERDMAN)
    Organism Taxid: 652616
    Strain: ATCC 35801 / TMC 107 / ERDMAN
    Synonym: ICL1,ISOCITRASE,ISOCITRATASE,METHYLISOCITRATE LYASE,MICA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2VGX4Ligand/Ion4-HYDROXY-2-OXOBUTANOIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:153 , HOH A:604 , HOH A:647 , HOH A:787 , HOH A:879binding site for residue MG A 501
2AC2SOFTWAREALA A:276 , ALA A:279 , GLN A:308 , HOH A:666 , HOH A:669 , HOH A:869binding site for residue MG A 502
3AC3SOFTWARETRP A:93 , ASP A:108 , CYS A:191 , GLY A:192 , HIS A:193 , ASN A:313 , SER A:315 , SER A:317 , THR A:347 , LEU A:348 , HOH A:603 , HOH A:787binding site for residue VGX A 503
4AC4SOFTWAREASP B:108 , ASP B:153 , HOH B:637 , HOH B:674 , HOH B:694 , HOH B:699 , HOH B:855binding site for residue MG B 501
5AC5SOFTWAREASP C:108 , ASP C:153 , HOH C:616 , HOH C:696 , HOH C:698 , HOH C:766 , HOH C:821binding site for residue MG C 501
6AC6SOFTWARETRP D:93 , ASP D:108 , ASP D:153 , HOH D:602 , HOH D:659 , HOH D:666 , HOH D:724 , HOH D:818binding site for residue MG D 501
7AC7SOFTWAREGLN A:394 , TRP B:93 , ASP B:108 , LYS B:190 , GLY B:192 , HIS B:193 , LEU B:194 , ASN B:313 , SER B:315 , SER B:317 , THR B:347 , LEU B:348 , HOH B:641 , HOH B:694binding site for Di-peptide VGX B 502 and CYS B 191
8AC8SOFTWARETRP C:93 , ASP C:108 , LYS C:190 , GLY C:192 , HIS C:193 , LEU C:194 , ASN C:313 , SER C:315 , SER C:317 , THR C:347 , LEU C:348 , HOH C:605 , GLN D:394binding site for Di-peptide VGX C 502 and CYS C 191
9AC9SOFTWAREGLN C:394 , TRP D:93 , ASP D:108 , LYS D:190 , GLY D:192 , HIS D:193 , LEU D:194 , ASN D:313 , SER D:315 , SER D:317 , THR D:347binding site for Di-peptide VGX D 502 and CYS D 191

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DQL)

(-) 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:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhh...eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhh....eeeeee......ee.......hhh.eeeee.....eee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dql A   1 MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQF 427
                                    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       


Chain B from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhh...eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhh....eeeeee......ee.......hhh.eeeee.....eee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dql B   1 MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQF 427
                                    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       


Chain C from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhh...eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhh....eeeeee......ee.......hhh.eeeee.....eee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dql C   1 MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQF 427
                                    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       


Chain D from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh....eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh...........eeee......hhhhhhhhhhhhhhh...eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhh....eeeeee......ee.......hhh.eeeee.....eee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh.....eeeee.....hhhhh.hhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dql D   1 MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQF 427
                                    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
   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 5DQL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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