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(-) Description

Title :  1.4A CRYSTAL STRUCTURE OF ISOCITRATE LYASE FROM YERSINIA PESTIS CO92
 
Authors :  S. S. Sharma, J. S. Brunzelle, T. Skarina, A. Savchenko, W. F. Anderson, For Structural Genomics Of Infectious Diseases (Csgid)
Date :  19 Jan 10  (Deposition) - 14 Apr 10  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Isocitrate Lyase, Conserved, Cd, Proteomics Evidence (Cytoplasmid Or Periplasmic), Drug Target Functions, Lyase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Sharma, J. S. Brunzelle, Z. Wawrzak, T. Skarina, E. Gordon, A. Savchenko, W. F. Anderson
1. 4A Crystal Structure Of Isocitrate Lyase From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOCITRATE LYASE
    Chains: A, B
    EC Number: 4.1.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 CODONPLUS(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ACEA, Y0016, YPO3725, YP_3087
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: CO92

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric Unit (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 36)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LG3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LG3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LG3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LG3)

(-) Exons   (0, 0)

(no "Exon" information available for 3LG3)

(-) Sequences/Alignments

Asymmetric 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:419
 aligned with Q7CLE1_YERPE | Q7CLE1 from UniProtKB/TrEMBL  Length:435

    Alignment length:419
                                    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         
         Q7CLE1_YERPE     1 MTISRTQQIQQLEQEWTSPRWKNITRPYSAEDVIKLRGSVNPECTFAQNGAKKLWELLHGGSRKGYINCLGALTGGQALQQAKAGVEAIYMSGWQVAADANTASSMYPDQSLYPVDSVPAVVKRINNSFRRADQIQWSNNIEPGSKGYTDYFLPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEAIQKLVAARLAADVLGVPTLLIARTDADAADLLTSDCDPYDREFITGDRTAEGFFRTRAGIEQAISRGLAYAPYADLVWCETSTPDLALAKRFADAVHAQFPGKLLAYNCSPSFNWKKNLTDQQIASFQDELSAMGYKYQFITLAGIHSMWFNMFDLAHAYAQGEGMKHYVEKVQQPEFASVDRGYTFASHQQEVGTGYFDKVTNIIQGG 419
               SCOP domains d3lg3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhh...eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh...............eeee......hhhhhhhhhhhhhhhh..eeeee..hhhhh........ee.hhhhhhhhhhhhhhhhhhhh...eeeeee......ee....hhhhhh.eeeee.....eee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg3 A   1 mTISRTQQIQQLEQEWTSPRWKNITRPYSAEDVIKLRGSVNPECTFAQNGAKKLWELLHGGSRKGYINCLGALTGGQALQQAKAGVEAIYmSGWQVAADANTASSmYPDQSLYPVDSVPAVVKRINNSFRRADQIQWSNNIEPGSKGYTDYFLPIVADAEAGFGGVLNAFELmKAmIEAGAAGVHFEDQLAAVKKCGHmGGKVLVPTQEAIQKLVAARLAADVLGVPTLLIARTDADAADLLTSDCDPYDREFITGDRTAEGFFRTRAGIEQAISRGLAYAPYADLVWCETSTPDLALAKRFADAVHAQFPGKLLAYNCSPSFNWKKNLTDQQIASFQDELSAmGYKYQFITLAGIHSmWFNmFDLAHAYAQGEGmKHYVEKVQQPEFASVDRGYTFASHQQEVGTGYFDKVTNIIQGG 419
                            |       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         
                            |                                                                                        91-MSE        106-MSE                                                            173-MSE                   199-MSE                                                                                                                                          344-MSE        359-MSE          376-MSE                                       
                            1-MSE                                                                                                                                                                        176-MSE                                                                                                                                                                                    363-MSE                                                    


Chain B from PDB  Type:PROTEIN  Length:414
 aligned with Q7CLE1_YERPE | Q7CLE1 from UniProtKB/TrEMBL  Length:435

    Alignment length:417
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       
         Q7CLE1_YERPE     2 TISRTQQIQQLEQEWTSPRWKNITRPYSAEDVIKLRGSVNPECTFAQNGAKKLWELLHGGSRKGYINCLGALTGGQALQQAKAGVEAIYMSGWQVAADANTASSMYPDQSLYPVDSVPAVVKRINNSFRRADQIQWSNNIEPGSKGYTDYFLPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEAIQKLVAARLAADVLGVPTLLIARTDADAADLLTSDCDPYDREFITGDRTAEGFFRTRAGIEQAISRGLAYAPYADLVWCETSTPDLALAKRFADAVHAQFPGKLLAYNCSPSFNWKKNLTDQQIASFQDELSAMGYKYQFITLAGIHSMWFNMFDLAHAYAQGEGMKHYVEKVQQPEFASVDRGYTFASHQQEVGTGYFDKVTNIIQG 418
               SCOP domains d3lg3b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ICL-3lg3B01 B:256-418                                                                                                                                               Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ICL-3lg3B02 B:256-418                                                                                                                                               Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ICL-3lg3B03 B:256-418                                                                                                                                               Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ICL-3lg3B04 B:256-418                                                                                                                                               Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhh...eeehhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh...............eeee......hhhhhhhhhhhhhhhh..eeeee..hhhhh..---...ee.hhhhhhhhhhhhhhhhhhhh...eeeeee......ee....hhhhhh.eeeee.....eee..hhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg3 B   2 TISRTQQIQQLEQEWTSPRWKNITRPYSAEDVIKLRGSVNPECTFAQNGAKKLWELLHGGSRKGYINCLGALTGGQALQQAKAGVEAIYmSGWQVAADANTASSmYPDQSLYPVDSVPAVVKRINNSFRRADQIQWSNNIEPGSKGYTDYFLPIVADAEAGFGGVLNAFELmKAmIEAGAAGVHFEDQLAAVKKC---GGKVLVPTQEAIQKLVAARLAADVLGVPTLLIARTDADAADLLTSDCDPYDREFITGDRTAEGFFRTRAGIEQAISRGLAYAPYADLVWCETSTPDLALAKRFADAVHAQFPGKLLAYNCSPSFNWKKNLTDQQIASFQDELSAmGYKYQFITLAGIHSmWFNmFDLAHAYAQGEGmKHYVEKVQQPEFASVDRGYTFASHQQEVGTGYFDKVTNIIQG 418
                                    11        21        31        41        51        61        71        81        91       101    |  111       121       131       141       151       161       171 |  |  181       191    |  201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  |    351       361 |     371    |  381       391       401       411       
                                                                                                                    91-MSE        106-MSE                                                            173-MSE                196 200                                                                                                                                             344-MSE        359-MSE          376-MSE                                      
                                                                                                                                                                                                        176-MSE                                                                                                                                                                                    363-MSE
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LG3)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PK_TIM (63)
(-)
Family: ICL (3)
(-)
Yersinia pestis (1)
1aICL-3lg3B01B:256-418
1bICL-3lg3B02B:256-418
1cICL-3lg3B03B:256-418
1dICL-3lg3B04B:256-418

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7CLE1_YERPE | Q7CLE1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004451    isocitrate lyase activity    Catalysis of the reaction: isocitrate = glyoxylate + succinate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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