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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME AVIAN ATIC IN COMPLEX WITH AICAR AND XMP AT 1.93 ANGSTROMS.
 
Authors :  D. W. Wolan, S. E. Greasly, G. P. Beardsley, I. A. Wilson
Date :  29 Jul 02  (Deposition) - 07 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, 2 Functional Domains; Impch Domain = Alpha/Beta/Alpha; Aicar Tfase = 2 Alpha/Beta/Alpha Domains, 1 Alpha + Beta Domain, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Wolan, S. E. Greasly, G. P. Beardsley, I. A. Wilson
Structural Insights Into The Avian Aicar Transformylase Mechanism.
Biochemistry V. 41 15505 2002
PubMed-ID: 12501179  |  Reference-DOI: 10.1021/BI020505X

(-) Compounds

Molecule 1 - AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
    Chains: A, B
    EC Number: 2.1.2.3, 3.5.4.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PURH
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (AICAR TRANSFORMYLASE) AND IMP CYCLOHYDROLASE (INOSINICASE, IMP SYNTHETASE, ATIC)]

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1AMZ2Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
2K2Ligand/IonPOTASSIUM ION
3XMP2Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:426 , THR A:429 , SER A:431 , SER A:433 , ASP A:540 , LEU A:590 , HIS A:592BINDING SITE FOR RESIDUE K A 594
2AC2SOFTWAREVAL B:426 , THR B:429 , SER B:431 , SER B:433 , ASP B:540 , LEU B:590 , HIS B:592BINDING SITE FOR RESIDUE K B 594
3AC3SOFTWAREARG A:208 , TYR A:209 , ILE A:239 , ASN A:240 , LYS A:267 , HIS A:268 , GLY A:317 , ASP A:340 , HOH A:1004 , HOH A:1005 , HOH A:1013 , HOH A:1022 , HOH A:1054 , HOH A:1080 , HOH A:1136 , HOH A:1145 , HOH A:1161 , ALA B:541 , PHE B:542 , ARG B:589 , PHE B:591BINDING SITE FOR RESIDUE AMZ A 1001
4AC4SOFTWAREPHE A:542 , ARG A:589 , ARG B:208 , TYR B:209 , ILE B:239 , ASN B:240 , LYS B:267 , HIS B:268 , GLY B:317 , ASP B:340 , HOH B:1005 , HOH B:1006 , HOH B:1008 , HOH B:1017 , HOH B:1028 , HOH B:1042BINDING SITE FOR RESIDUE AMZ B 1002
5AC5SOFTWARESER A:11 , VAL A:12 , SER A:13 , LYS A:15 , SER A:35 , GLY A:37 , THR A:38 , GLY A:64 , ARG A:65 , LYS A:67 , THR A:68 , LEU A:69 , CYS A:102 , ASN A:103 , LEU A:104 , TYR A:105 , ASP A:126 , ILE A:127 , GLY A:128 , GLY A:129BINDING SITE FOR RESIDUE XMP A 1003
6AC6SOFTWARESER B:11 , VAL B:12 , SER B:13 , LYS B:15 , SER B:35 , GLY B:37 , THR B:38 , GLY B:64 , ARG B:65 , LYS B:67 , THR B:68 , CYS B:102 , ASN B:103 , LEU B:104 , TYR B:105 , ASP B:126 , ILE B:127 , GLY B:128 , GLY B:129 , HOH B:1036BINDING SITE FOR RESIDUE XMP B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M9N)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:216 -Pro A:217
2Ser A:431 -Asn A:432
3Ser B:216 -Pro B:217
4Ser B:431 -Asn B:432

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M9N)

(-) Exons   (0, 0)

(no "Exon" information available for 1M9N)

(-) 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:590
 aligned with PUR9_CHICK | P31335 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:590
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593
           PUR9_CHICK     4 RQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH 593
               SCOP domains d1m9na1 A:4-200 IMP cyclohydrolase domain of bifunctional purine biosynthesis enzyme ATIC                                                                                                            d1m9na2 A:201-593 AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m9nA04 A:4-200  [code=3.40.50.1380, no name defined]                                                                                                                                                ---------------------------1m9nA03 A:228-374  [code=3.40.140.20, no name defined]                                                                                             1m9nA02 A:375-476,A:520-583  [code=3.40.140.20, no name defined]                                      -1m9nA01 A:478-519                         1m9nA02 A:375-476,A:520-583  [code=3.40.140.20, no name defined]---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhh...eeeehhhhhhhhhhh...eeehhhhhh............hhhhhhhhhh..hhhhhhhhhhhh...eeeeeee..hhhhhhhh...hhhhhhhh..hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee...........eeee.......eeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeee....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh.eeeee........eeeeee..eeeeee......hhhhhh.........hhhhhhhhhhhhhhhhh.....eeeee..eeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhh.ee....hhhhhhhhhhhhhhh....hhhhhhhhh.eee.....hhhhhhhhhh....eeeee......hhhhhhhhh..eeeeeee....hhhhhhhhhhhh..eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m9n A   4 RQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH 593
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593


Chain B from PDB  Type:PROTEIN  Length:590
 aligned with PUR9_CHICK | P31335 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:590
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593
           PUR9_CHICK     4 RQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH 593
               SCOP domains d1m9nb1 B:4-200 IMP cyclohydrolase domain of bifunctional purine biosynthesis enzyme ATIC                                                                                                            d1m9nb2 B:201-593 AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m9nB04 B:4-200  [code=3.40.50.1380, no name defined]                                                                                                                                                ---------------------------1m9nB03 B:228-374  [code=3.40.140.20, no name defined]                                                                                             1m9nB02 B:375-476,B:520-583  [code=3.40.140.20, no name defined]                                      -1m9nB01 B:478-519                         1m9nB02 B:375-476,B:520-583  [code=3.40.140.20, no name defined]---------- CATH domains
           Pfam domains (1) -------------MGS-1m9nB03 B:17-131                                                                                               ----AICARFT_IMPCHas-1m9nB01 B:136-463                                                                                                                                                                                                                                                                                                       ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------MGS-1m9nB04 B:17-131                                                                                               ----AICARFT_IMPCHas-1m9nB02 B:136-463                                                                                                                                                                                                                                                                                                       ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh....eehhhhhh............hhhhhhhhhh..hhhhhhhhhhhh...eeeeeee..hhhhhh.....hhhhhhhh..hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee...........eeee.......eeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeee....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh.eeeee........eeeeee..eeeeee......hhhhhh.........hhhhhhhhhhhhhhhhh.....eeeee..eeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhh.ee....hhhhhhhhhhhhhhh....hhhhhhhhh.eee.....hhhhhhhhhhh...eeeee......hhhhhhhhh..eeeeeee....hhhhhhhhhhhhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m9n B   4 RQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH 593
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593
   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  (2, 4)

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

(-) CATH Domains  (3, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: CDA (39)
(-)
Clan: no clan defined [family: MGS] (13)
(-)
Family: MGS (13)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PUR9_CHICK | P31335)
molecular function
    GO:0003937    IMP cyclohydrolase activity    Catalysis of the reaction: IMP + H2O = 5-formamido-1-(5-phosphoribosyl)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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004643    phosphoribosylaminoimidazolecarboxamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide = tetrahydrofolate + 5'-phosphoribosyl-5-formamido-4-imidazolecarboxamide.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    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:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of 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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1m9n
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PUR9_CHICK | P31335: 1g8m 1oz0 1thz 2b1g 2b1i 2iu0 2iu3

(-) Related Entries Specified in the PDB File

1g8m CRYSTAL STRUCTURE OF AVIAN ATIC, A BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME IN PURINE BIOSYNTHESIS AT 1.75 ANG. RESOLUTION