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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBHISA FROM THE THERMOPHILE CORYNEBACTERIUM EFFICIENS
 
Authors :  L. Noda-Garcia, A. R. Camacho-Zarco, S. Medina-Ruiz, E. A. Verduzco-C P. Gaytan, M. Carrillo-Tripp, V. Fulop, F. Barona-Gomez
Date :  13 Jun 12  (Deposition) - 26 Jun 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isomerase, (Beta-Alpha)8-Barrel, Metabolism, Evolution Of Substrate Specificity, Histidine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Noda-Garcia, A. R. Camacho-Zarco, S. Medina-Ruiz, P. Gaytan, M. Carrillo-Tripp, V. Fulop, F. Barona-Gomez
Evolution Of Substrate Specificity In A Recipient'S Enzyme Following Horizontal Gene Transfer.
Mol. Biol. Evol. V. 30 2024 2013
PubMed-ID: 23800623  |  Reference-DOI: 10.1093/MOLBEV/MST115

(-) Compounds

Molecule 1 - 1-(5-PHOSPHORIBOSYL)-5-((5'-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO)IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22-CEFF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEBACTERIUM EFFICIENS
    Organism Taxid: 152794
    Synonym: PHOSPHORIBOSYL ISOMERASE, SUBHISA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:52 , ALA A:55 , SER A:61 , HIS A:63 , GLY A:81 , ARG A:91BINDING SITE FOR RESIDUE GOL A1249
2AC2SOFTWAREASP B:52 , ALA B:55 , SER B:61 , HIS B:63 , GLY B:81 , GLY B:82 , ARG B:91BINDING SITE FOR RESIDUE GOL B1251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AXK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AXK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AXK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AXK)

(-) Exons   (0, 0)

(no "Exon" information available for 4AXK)

(-) 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:236
 aligned with HIS4_COREF | Q8FNZ7 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:247
                                                                                                                                                                                                                                                                              246  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    |  
           HIS4_COREF     2 TFTILPAVDVVNGQAVRLDQGEAGTEKSYGTPLESALRWQEQGAEWLHFVDLDAAFNRGSNHELMAEITRQLDIKVELTGGIRDDASLERALATGATRVNIGTAALEKPEWIADVIRRHGEKIAVDIAVRLENGEWRTKGNGWVSDGGDLWEVLERLDSQGCSRFVVTDVSKDGTLTGPNVDLLRDVAAATDAPIVASGGISTLEDVLGLAKYQDEGIDSVIIGKALYEHRFTLAEALEAVEKLG--   -
               SCOP domains d4axka_ A: automated        matches                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....ee....-------.eehhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee.........----...hhhhhhhhhhhh....eeeee.hhhhh....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh.eeeeeehhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axk A   2 TFTILPAVDVVNGQAVRLDQ-------SYGTPLESALRWQEQGAEWLHFVDLDAAFNRGSNHELMAEITRQLDIKVELTGGIRDDASLERALATGATRVNIGTAALEKPEWIADVIRRHGEKIAVDIAVRLENGEWRTKGN----DGGDLWEVLERLDSQGCSRFVVTDVSKDGTLTGPNVDLLRDVAAATDAPIVASGGISTLEDVLGLAKYQDEGIDSVIIGKALYEHRFTLAEALEAVEKLGKL 248
                                    11        21       |31        41        51        61        71        81        91       101       111       121       131       141|    | 151       161       171       181       191       201       211       221       231       241       
                                              21      29                                                                                                              142  147                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:239
 aligned with HIS4_COREF | Q8FNZ7 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:249
                                                                                                                                                                                                                                                                              246    
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    |    
           HIS4_COREF     2 TFTILPAVDVVNGQAVRLDQGEAGTEKSYGTPLESALRWQEQGAEWLHFVDLDAAFNRGSNHELMAEITRQLDIKVELTGGIRDDASLERALATGATRVNIGTAALEKPEWIADVIRRHGEKIAVDIAVRLENGEWRTKGNGWVSDGGDLWEVLERLDSQGCSRFVVTDVSKDGTLTGPNVDLLRDVAAATDAPIVASGGISTLEDVLGLAKYQDEGIDSVIIGKALYEHRFTLAEALEAVEKLG----   -
               SCOP domains d4axkb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....ee............eehhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeeeee.eee..eee.----------hhhhhhhhhhhh....eeee...........hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh.eeeeeehhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axk B   2 TFTILPAVDVVNGQAVRLDQGEAGTEKSYGTPLESALRWQEQGAEWLHFVDLDAAFNRGSNHELMAEITRQLDIKVELTGGIRDDASLERALATGATRVNIGTAALEKPEWIADVIRRHGEKIAVDIAVRLENGEWRT----------DLWEVLERLDSQGCSRFVVTDVSKDGTLTGPNVDLLRDVAAATDAPIVASGGISTLEDVLGLAKYQDEGIDSVIIGKALYEHRFTLAEALEAVEKLGKLAA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       | -       151       161       171       181       191       201       211       221       231       241         
                                                                                                                                                                   139        150
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AXK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AXK)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HIS4_COREF | Q8FNZ7)
molecular function
    GO:0003949    1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity    Catalysis of the reaction: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004640    phosphoribosylanthranilate isomerase activity    Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    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.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
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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