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(-) Description

Title :  STRUCTURE OF FORMYLGLYCINAMIDE SYNTHETASE
 
Authors :  S. E. Ealick, R. Anand, A. A. Hoskin, J. Stubbe
Date :  27 Apr 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Purl, Fgam Synthetase, Purs, Purq, Formyl Glycinamide, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Anand, A. A. Hoskin, J. Stubbe, S. E. Ealick
Domain Organization Of Salmonella Typhimurium Formylglycinamide Ribonucleotide Amidotransferase Revealed By X-Ray Crystallography
Biochemistry V. 43 10328 2004
PubMed-ID: 15301531  |  Reference-DOI: 10.1021/BI0491301
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE
    Chains: A
    EC Number: 6.3.5.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURL, STM2565
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: FGAM SYNTHASE, FGAMS, FORMYLGLYCINAMIDE RIBOTIDE AMIDOTRANSFERASE, FGARAT, FORMYLGLYCINAMIDE RIBOTIDE SYNTHETASE, FORMYLGLYCINAMIDE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CYG1Mod. Amino Acid2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC ACID
3MG3Ligand/IonMAGNESIUM ION
4SO46Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:679 , ASN A:722 , ASP A:884 , ADP A:2005 , HOH A:3086 , HOH A:3089BINDING SITE FOR RESIDUE MG A 2006
02AC2SOFTWAREGLU A:718 , ADP A:2005 , HOH A:2023 , HOH A:2054 , HOH A:3090 , HOH A:3091BINDING SITE FOR RESIDUE MG A 2007
03AC3SOFTWAREADP A:2005 , HOH A:2041 , HOH A:3085 , HOH A:3087 , HOH A:3088BINDING SITE FOR RESIDUE MG A 2008
04AC4SOFTWAREHIS A:216 , GLU A:294 , GLY A:504 , ALA A:505 , LYS A:776 , HOH A:2608BINDING SITE FOR RESIDUE SO4 A 2001
05AC5SOFTWAREHIS A:216 , THR A:295 , HIS A:296 , ASN A:297 , HIS A:298 , SER A:778 , HOH A:2261 , HOH A:2269 , HOH A:2362 , HOH A:2733 , HOH A:2914BINDING SITE FOR RESIDUE SO4 A 2002
06AC6SOFTWARETYR A:690 , ARG A:812 , LYS A:1228 , VAL A:1229 , HOH A:2066 , HOH A:2527 , HOH A:2765 , HOH A:2963BINDING SITE FOR RESIDUE SO4 A 2009
07AC7SOFTWAREGLN A:1176 , GLN A:1183 , GLY A:1184 , MET A:1185 , VAL A:1186 , HOH A:2245 , HOH A:2252 , HOH A:2785 , HOH A:3012BINDING SITE FOR RESIDUE SO4 A 2010
08AC8SOFTWAREPRO A:1040 , LYS A:1041 , HIS A:1086 , HOH A:2274 , HOH A:2415 , HOH A:2621 , HOH A:2704 , HOH A:2836BINDING SITE FOR RESIDUE SO4 A 2011
09AC9SOFTWAREHIS A:1086 , ARG A:1126 , PRO A:1127 , GLN A:1128 , THR A:1129 , HOH A:2244 , HOH A:2250 , HOH A:2792 , HOH A:2974BINDING SITE FOR RESIDUE SO4 A 2012
10BC1SOFTWARETHR A:386 , GLY A:387 , TYR A:388 , PHE A:389 , LEU A:652 , GLN A:668 , PRO A:676 , ALA A:678 , ASP A:679 , GLU A:718 , ASN A:722 , SER A:886 , MG A:2006 , MG A:2007 , MG A:2008 , HOH A:2023 , HOH A:2041 , HOH A:2061 , HOH A:2093 , HOH A:2140 , HOH A:2156 , HOH A:2265 , HOH A:2381 , HOH A:2682 , HOH A:3090 , HOH A:3091BINDING SITE FOR RESIDUE ADP A 2005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T3T)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:1233 -Pro A:1234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T3T)

(-) Exons   (0, 0)

(no "Exon" information available for 1T3T)

(-) 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:1284
 aligned with PUR4_SALTY | P74881 from UniProtKB/Swiss-Prot  Length:1295

    Alignment length:1303
                                    1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292   
          PUR4_SALTY      - --------MMEILRGSPALSAFRINKLLARFQAANLQVHNIYAEYVHFADLNAPLNDSEQAQLTRLLQYGPALSSHTPAGKLLLVTPRPGTISPWSSKATDIAHNCGLQQVDRLERGVAYYIEASTLTAEQWRQVAAELHDRMMETVFSSLTDAEKLFIHHQPAPVSSVDLLGEGRQALIDANLRLGLALAEDEIDYLQEAFTKLGRNPNDIELYMFAQANSEHCRHKIFNADWIIDGKPQPKSLFKMIKNTFETTPDYVLSAYKDNAAVMEGSAVGRYFADHNTGRYDFHQEPAHILMKVETHNHPTAISPWPGAATGSGGEIRDEGATGRGAKPKAGLVGFSVSNLRIPGFEQPWEEDFGKPERIVTALDIMTEGPLGGAAFNNEFGRPALTGYFRTYEEKVNSHNGEELRGYHKPIMLAGGIGNIRADHVQKGEIVVGAKLIVLGGPAMNIGLGGGAASSMASGQSDADLDFASVQRDNPEMERRCQEVIDRCWQLGDANPILFIHDVGAGGLSNAMPELVSDGGRGGKFELRDILSDEPGMSPLEIWCNESQERYVLAVAADQLPLFDELCKRERAPYAVIGDATEEQHLSLHDNHFDNQPIDLPLDVLLGKTPKMTRDVQTLKAKGDALNRADITIADAVKRVLHLPTVAEKTFLVTIGDRTVTGMVARDQMVGPWQVPVADCAVTTASLDSYYGEAMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDAGLYDAVKAVGEELCPQLGLTIPVGKDSMSMKTRWQEGNEQREMTSPLSLVISAFARVEDVRHTLTPQLSTEDNALLLIDLGKGHNALGATALAQVYRQLGDKPADVRDVAQLKGFYDAMQALVAARKLLAWHDRSDGGLLVTLAEMAFAGHCGVQVDIAALGDDHLAALFNEELGGVIQVRAEDRDAVEALLAQYGLADCVHYLGQALAGDRFVITANDQTVFSESRTTLRVWWAETTWQMQRLRDNPQCADQEHEAKANDTDPGLNVKLSFDINEDIAAPYIATGARPKVAVLREQGVNSHVEMAAAFHRAGFDAIDVHMSDLLGGRIGLGNFHALVACGGFSYGDVLGAGEGWAKSILFNHRVRDEFETFFHRPQTLALGVCNGCQMMSNLRELIPGSELWPRFVRNHSDRFEARFSLVEVTQSPSLLLQGMVGSQMPIAVSHGEGRVEVRDDAHLAALESKGLVALRYVDNFGKVTETYPANPNGSPNGITAVTTENGRVTIMMPHPERVFRTVANSWHPENWGEDSPWMRIFRNARKQLG 1295
               SCOP domains --------d1t3ta3 A:1-152 FGAM synthase PurL, PurS-like domain                                                                                                    d1t3ta1 A:153-220 FGAM synthase PurL, linker domain                 d1t3ta4 A:221-429 FGAM synthase PurL, PurM-like module, N1 and N2 domains                                                                                                                                        d1t3ta6 A:430-616                    FGAM synthase PurL, PurM-like module, C1 and C2 domains                                                                                               d1t3ta5 A:617-816 FGAM synthase PurL, PurM-like module, N1 and N2 domains                                                                                                                               d1t3ta7 A:817-1033 FGAM synthase PurL, PurM-like module, C1 and C2 domains                                                                                                                                               d1t3ta2 A:1034-1295 FGAM synthase PurL, amidotransferase domain                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS-1t3tA02 A:257-389                                                                                                               -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-1t3tA03 A:821-969                                                                                                                             ---------------------------------------------------------------------GATase_5-1t3tA01 A:1039-1293                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-1t3tA04 A:821-969                                                                                                                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee..eeeeeeeeee..hhhhhhhhhhhhhh......eeeeeeeeeeee....hhhhhhhhhhhh.............eeeeeee.....hhhhhhhhhhhhhh....eeeeeeeeeeeee....hhhhhhhhhhh......eeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhheeee..eee..hhhhhhhhhhhhh...eee......eeeeeeeeeeeee......eeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......................hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.eeeeee..eeeeee....eeeeeeeeeehhhhh.........eeeeee.......-------------------.......hhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeee.hhh.......hhhhhhhh....eeeeee...hhhhhhhhhhhhh..eeeeeeee...eeeeee....eeeeeeehhhhh......eeee...............hhhhhhhhhh.......hhhhhh.........eee..ee....ee....eeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhh.eeeeeee......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...eeeee....eeeee...eeeeeeeeee.hhhhh.........eeeeeee..........hhhhhhh...........hhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh.eeeee.hhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.eeeeeeee...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhh.....eeeeee.....hhhhhhhhhhhh..eeeeeehhhhhh...hhhhh.eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh.......eee.......eeeeeeeee....hhhhh.....eeeeeeee...eee..hhhhhhhhhhh..eeeee.................hhh.eeeee.....eeee..hhhhh.hhhhh............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t3t A   -7 GLVPRGSHMMEILRGSPALSAFRINKLLARFQAANLQVHNIYAEYVHFADLNAPLNDSEQAQLTRLLQYGPALSSHTPAGKLLLVTPRPGTISPWSSKATDIAHNCGLQQVDRLERGVAYYIEASTLTAEQWRQVAAELHDRMMETVFSSLTDAEKLFIHHQPAPVSSVDLLGEGRQALIDANLRLGLALAEDEIDYLQEAFTKLGRNPNDIELYMFAQANSEHCRHKIFNADWIIDGKPQPKSLFKMIKNTFETTPDYVLSAYKDNAAVMEGSAVGRYFADHNTGRYDFHQEPAHILMKVETHNHPTAISPWPGAATGSGGEIRDEGATGRGAKPKAGLVGFSVSNLRIPGFEQPWEEDFGKPERIVTALDIMTEGPLGGAAFNNEFGRPALTGYFRTYEEKVNSHNGEELRGYHKPIMLAGGIGNIRADHVQKGEIVVGAKLIVLGGPAMNIG-------------------FASVQRDNPEMERRCQEVIDRCWQLGDANPILFIHDVGAGGLSNAMPELVSDGGRGGKFELRDILSDEPGMSPLEIWCNESQERYVLAVAADQLPLFDELCKRERAPYAVIGDATEEQHLSLHDNHFDNQPIDLPLDVLLGKTPKMTRDVQTLKAKGDALNRADITIADAVKRVLHLPTVAEKTFLVTIGDRTVTGMVARDQMVGPWQVPVADCAVTTASLDSYYGEAMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDAGLYDAVKAVGEELCPQLGLTIPVGKDSMSMKTRWQEGNEQREMTSPLSLVISAFARVEDVRHTLTPQLSTEDNALLLIDLGKGHNALGATALAQVYRQLGDKPADVRDVAQLKGFYDAMQALVAARKLLAWHDRSDGGLLVTLAEMAFAGHCGVQVDIAALGDDHLAALFNEELGGVIQVRAEDRDAVEALLAQYGLADCVHYLGQALAGDRFVITANDQTVFSESRTTLRVWWAETTWQMQRLRDNPQCADQEHEAKANDTDPGLNVKLSFDINEDIAAPYIATGARPKVAVLREQGVNSHVEMAAAFHRAGFDAIDVHMSDLLGGRIGLGNFHALVACGGFSYGDVLGAGEGWAKSILFNHRVRDEFETFFHRPQTLALGVcNGCQMMSNLRELIPGSELWPRFVRNHSDRFEARFSLVEVTQSPSLLLQGMVGSQMPIAVSHGEGRVEVRDDAHLAALESKGLVALRYVDNFGKVTETYPANPNGSPNGITAVTTENGRVTIMMPHPERVFRTVANSWHPENWGEDSPWMRIFRNARKQLG 1295
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442    |    -         -    |  472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132  |   1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                447                 467                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        1135-CYG
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (5, 7)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1T3T)

(-) Pfam Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Clan: Glutaminase_I (73)
(-)
Clan: no clan defined [family: AIRS] (11)
(-)
Clan: no clan defined [family: AIRS_C] (13)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR4_SALTY | P74881)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004642    phosphoribosylformylglycinamidine synthase activity    Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H(2)O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H(+) + phosphate.
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:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    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.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
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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  1t3t
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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR4_SALTY | P74881: 3ugj 3ujn 3umm 4l78 4lgy 4mgh 4r7g

(-) Related Entries Specified in the PDB File

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