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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY
 
Authors :  E. A. Toth, T. O. Yeates, E. Goedken, J. E. Dixon, S. Marqusee
Date :  20 Dec 99  (Deposition) - 10 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Purine Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Toth, C. Worby, J. E. Dixon, E. R. Goedken, S. Marqusee, T. O. Yeates
The Crystal Structure Of Adenylosuccinate Lyase From Pyrobaculum Aerophilum Reveals An Intracellular Protein With Three Disulfide Bonds.
J. Mol. Biol. V. 301 433 2000
PubMed-ID: 10926519  |  Reference-DOI: 10.1006/JMBI.2000.3970
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLOSUCCINATE LYASE
    Chains: A, B, C, D
    EC Number: 4.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DOF)

(-) Sites  (0, 0)

(no "Site" information available for 1DOF)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:50
2A:49 -A:87
3A:167 -A:403
4B:37 -B:50
5B:49 -B:87
6B:167 -B:403
7C:37 -C:50
8C:49 -C:87
9C:167 -C:403
10D:37 -D:50
11D:49 -D:87
12D:167 -D:403

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DOF)

(-) 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:385
 aligned with Q8ZY28_PYRAE | Q8ZY28 from UniProtKB/TrEMBL  Length:403

    Alignment length:402
                                    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  
         Q8ZY28_PYRAE     2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEVYRLERETGHDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVERGGGSSAMPHKANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
               SCOP domains d1dofa_ A: Adenylosuccinate lyase                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dofA02 A:2-94 Fumarase/aspartase (N-terminal domain)                                        1dofA01 A:95-347 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         1dofA03 A:348-403 Fumarase/aspartase (C-terminal domain) CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......--------hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...---------..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dof A   2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEV--------HDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVEGG---------ANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
                                    11        21        31        41        51        61 |       -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
                                                                                        63       72                                                                                                                                                                                        259       269                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with Q8ZY28_PYRAE | Q8ZY28 from UniProtKB/TrEMBL  Length:403

    Alignment length:402
                                    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  
         Q8ZY28_PYRAE     2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEVYRLERETGHDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVERGGGSSAMPHKANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
               SCOP domains d1dofb_ B: Adenylosuccinate lyase                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dofB02 B:2-94 Fumarase/aspartase (N-terminal domain)                                        1dofB01 B:95-347 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         1dofB03 B:348-401                                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......--------hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...---------..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dof B   2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEV--------HDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVEGG---------ANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
                                    11        21        31        41        51        61 |       -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
                                                                                        63       72                                                                                                                                                                                        259       269                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:385
 aligned with Q8ZY28_PYRAE | Q8ZY28 from UniProtKB/TrEMBL  Length:403

    Alignment length:402
                                    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  
         Q8ZY28_PYRAE     2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEVYRLERETGHDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVERGGGSSAMPHKANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
               SCOP domains d1dofc_ C: Adenylosuccinate lyase                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dofC02 C:2-94 Fumarase/aspartase (N-terminal domain)                                        1dofC01 C:95-347 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         1dofC03 C:348-401                                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......--------hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...---------..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dof C   2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEV--------HDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVEGG---------ANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
                                    11        21        31        41        51        61 |       -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
                                                                                        63       72                                                                                                                                                                                        259       269                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:385
 aligned with Q8ZY28_PYRAE | Q8ZY28 from UniProtKB/TrEMBL  Length:403

    Alignment length:402
                                    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  
         Q8ZY28_PYRAE     2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEVYRLERETGHDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVERGGGSSAMPHKANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
               SCOP domains d1dofd_ D: Adenylosuccinate lyase                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dofD02 D:2-94 Fumarase/aspartase (N-terminal domain)                                        1dofD01 D:95-347 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         1dofD03 D:348-401                                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......--------hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...---------..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dof D   2 HVSPFDWRYGSEEIRRLFTNEAIINAYLEVERALVCALEELGVAERGCCEKVNKASVSADEV--------HDILSLVLLLEQKSGCRYVHYGATSNDIIDTAWALLIRRALAAVKEKARAVGDQLASMARKYKTLEMVGRTHGQWAEPITLGFKFANYYYELYIACRQLALAEEFIRAKIGGAVGTMASWGELGLEVRRRVAERLGLPHHVITTQVAPRESFAVLASALALMAAVFERLAVEIRELSRPEIGEVVEGG---------ANPTASERIVSLARYVRALTHVAFENVALWHERDLTNSANERVWIPEALLALDEILTSALRVLKNVYIDEERITENLQKALPYILTEFHMNRMIKEGASRAEAYKKAKEVKALTFEYQKWPVERLIEDALSLKLC 403
                                    11        21        31        41        51        61 |       -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
                                                                                        63       72                                                                                                                                                                                        259       269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (3, 12)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8ZY28_PYRAE | Q8ZY28)
molecular function
    GO:0070626    (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
    GO:0004018    N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
    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: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:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0009152    purine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1c3c T. MARITIMA ASL
1c3u T. MARITIMA ASL