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(-) Description

Title :  HISF PROTEIN FROM PYROBACULUM AEROPHILUM
 
Authors :  M. J. Banfield, J. S. Lott, A. A. Mccarthy, E. N. Baker
Date :  31 May 01  (Deposition) - 01 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Histidine Biosynthesis, Tim-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Banfield, J. S. Lott, V. Arcus, A. A. Mccarthy, E. N. Baker
Structure Of Hisf, A Histidine Biosynthetic Protein From Pyrobaculum Aerophilum
Acta Crystallogr. , Sect. D V. 57 1518 2001
PubMed-ID: 11679715  |  Reference-DOI: 10.1107/S0907444901012604
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL-21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773
    Other Details: RESIDUES 1-3 OF THE INTACT SEQUENCE ARE NOT PRESENT IN THE EXPRESSED PROTEIN

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:84 , GLY A:85 , VAL A:86 , ASN A:106 , THR A:107 , HOH A:2147 , HOH A:2148 , HOH A:2149 , HOH A:2150 , HOH A:2151 , HOH A:2152 , HOH A:2153BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREASP A:179 , GLY A:180 , GLY A:205 , GLY A:206 , ALA A:226 , ALA A:227 , SER A:228 , HOH A:2154 , HOH A:2155 , HOH A:2156 , HOH A:2157 , HOH A:2158BINDING SITE FOR RESIDUE PO4 A 302
3AC3SOFTWAREGLY B:84 , GLY B:85 , VAL B:86 , ASN B:106 , THR B:107 , HOH B:2104 , HOH B:2105 , HOH B:2106BINDING SITE FOR RESIDUE PO4 B 301
4AC4SOFTWAREASP B:179 , GLY B:180 , GLY B:206 , ALA B:226 , ALA B:227 , SER B:228 , HOH B:2071 , HOH B:2083 , HOH B:2107 , HOH B:2108 , HOH B:2109BINDING SITE FOR RESIDUE PO4 B 302
5AC5SOFTWAREASN A:106 , ALA A:131 , ASP A:133 , THR A:174 , GOL A:501 , HOH A:2150 , HOH A:2159BINDING SITE FOR RESIDUE GOL A 401
6AC6SOFTWARELYS A:22 , ASP A:133 , GLY A:147 , GLY A:148 , ASP A:179 , GOL A:401BINDING SITE FOR RESIDUE GOL A 501
7AC7SOFTWAREASN B:106 , ALA B:131 , ASP B:133 , THR B:174 , GOL B:501 , HOH B:2105 , HOH B:2110BINDING SITE FOR RESIDUE GOL B 401
8AC8SOFTWARELYS B:22 , GLY B:147 , ASP B:179 , GOL B:401BINDING SITE FOR RESIDUE GOL B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H5Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1H5Y)

(-) 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:252
 aligned with HIS6_PYRAE | Q8ZY16 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:252
                                    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  
           HIS6_PYRAE     2 DVALRIIPCLDIDGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGSQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVKRYLKERGVEVRI 253
               SCOP domains d1h5ya_ A: Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF                                                                                                                                                                           SCOP domains
               CATH domains 1h5yA00 A:2-253 Aldolase class I                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ....eeeeeeeehhhhhee.....hhhhhh--hhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeee...................hhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------eee---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h5y A   2 HMALRIIPCLDIDGGAKVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGSQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVKRYLKERGVEVRI 253
                                    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  


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with HIS6_PYRAE | Q8ZY16 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    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   
           HIS6_PYRAE     1 MDVALRIIPCLDIDGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGSQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVKRYLKERGVEVRI 253
               SCOP domains d1h5yb_ B: Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF                                                                                                                                                                            SCOP domains
               CATH domains 1h5yB00 B:1-253 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeehhhhhee.....hhhhheeehhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeee...................hhhhhhhhhhh...eeeeee..........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5y B   1 SHMALRIIPCLDIDGGAKVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGSQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVKRYLKERGVEVRI 253
                                    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
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H5Y)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HIS6_PYRAE | Q8ZY16)
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:0000107    imidazoleglycerol-phosphate synthase activity    Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+).
    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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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