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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE SYNTHETASE FROM FRANCISELLA TULARENSIS
 
Authors :  N. Maltseva, Y. Kim, J. Hasseman, W. F. Anderson, A. Joachimiak
Date :  17 Mar 10  (Deposition) - 14 Jul 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Fold, Csgid, Atp-Binding, Ligase, Nucleotide-Binding, Purine Biosynthesis, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maltseva, Y. Kim, J. Hasseman, W. F. Anderson, A. Joachimiak
Crystal Structure Of Phosphoribosylaminoimidazole Synthetas From Francisella Tularensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURM
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 177416
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 49)

Asymmetric/Biological Unit (6, 49)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3FMT2Ligand/IonFORMIC ACID
4MSE28Mod. Amino AcidSELENOMETHIONINE
5SO414Ligand/IonSULFATE ION
6TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:69 , ASN A:192 , GLY A:193 , TYR A:194 , SER A:195 , HOH A:364 , HOH A:379 , HOH A:388 , HOH A:394 , GLU B:7 , ASP B:8 , ALA B:9 , HOH B:420BINDING SITE FOR RESIDUE SO4 A 351
02AC2SOFTWAREASN A:192 , THR A:253 , GLY A:254 , HOH A:551 , HOH A:711 , HOH B:762BINDING SITE FOR RESIDUE SO4 A 352
03AC3SOFTWAREASN A:234 , HIS A:327 , ASN A:329 , HOH A:465 , HOH A:467 , HOH A:484 , HOH A:687 , ASN B:340BINDING SITE FOR RESIDUE SO4 A 353
04AC4SOFTWARESER A:41 , ASP A:107 , MSE A:119 , GLY A:140 , GLU A:141 , THR A:142 , HOH A:674 , HOH A:738 , HOH A:739 , HOH A:758BINDING SITE FOR RESIDUE AMP A 354
05AC5SOFTWARETHR A:32 , GLN A:33 , LYS B:343BINDING SITE FOR RESIDUE SO4 A 355
06AC6SOFTWAREALA A:143 , GLU A:144 , HOH A:649 , HOH A:675 , HOH B:676BINDING SITE FOR RESIDUE ACY A 356
07AC7SOFTWAREMSE A:76 , ARG A:198 , HOH A:380BINDING SITE FOR RESIDUE FMT A 357
08AC8SOFTWAREGLU A:14 , ALA A:15 , GLN A:18 , LYS B:29BINDING SITE FOR RESIDUE ACY A 359
09AC9SOFTWAREARG A:198 , HOH A:463 , HOH A:632 , GLY B:147BINDING SITE FOR RESIDUE SO4 A 348
10BC1SOFTWAREARG A:263 , HOH A:413 , GLY B:40 , SER B:41BINDING SITE FOR RESIDUE SO4 A 360
11BC2SOFTWAREASN B:-1 , ALA B:0 , HOH B:721 , HOH B:722BINDING SITE FOR RESIDUE FMT B 358
12BC3SOFTWARETHR B:69 , ASN B:192 , GLY B:193 , TYR B:194 , SER B:195 , HOH B:403 , HOH B:431 , HOH B:436 , HOH B:458 , HOH B:710 , HOH B:772BINDING SITE FOR RESIDUE SO4 B 351
13BC4SOFTWAREGLN A:150 , HOH A:557 , GLN B:150 , ALA B:151 , LYS B:176 , HOH B:456 , HOH B:615BINDING SITE FOR RESIDUE SO4 B 353
14BC5SOFTWAREPRO A:146 , LYS A:331 , HOH A:702 , GLN B:150 , HOH B:404BINDING SITE FOR RESIDUE SO4 B 354
15BC6SOFTWAREHOH A:464 , HOH A:545 , ARG B:300 , HOH B:484 , HOH B:659BINDING SITE FOR RESIDUE SO4 B 348
16BC7SOFTWAREASN B:192 , THR B:253 , GLY B:254BINDING SITE FOR RESIDUE SO4 B 359
17BC8SOFTWAREHOH A:555 , SER B:-2 , GLN B:25 , LYS B:28BINDING SITE FOR RESIDUE SO4 B 361
18BC9SOFTWARESER B:294 , GLU B:295 , HOH B:428 , HOH B:642BINDING SITE FOR RESIDUE SO4 B 362
19CC1SOFTWAREPHE B:42 , ASP B:107 , VAL B:123 , LEU B:137 , HOH B:709BINDING SITE FOR RESIDUE ACY B 363
20CC2SOFTWAREGLU A:177 , ASN B:234 , LYS B:326 , HIS B:327 , THR B:328 , ASN B:329 , HOH B:373 , HOH B:381 , HOH B:627 , HOH B:743 , HOH B:744BINDING SITE FOR RESIDUE TRS B 364
21CC3SOFTWAREPHE B:278 , ALA B:279 , THR B:280 , LYS B:285 , HOH B:384 , HOH B:485 , HOH B:582 , HOH B:805BINDING SITE FOR RESIDUE SO4 B 365

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M84)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M84)

(-) Exons   (0, 0)

(no "Exon" information available for 3M84)

(-) 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:348
 aligned with Q5NGF2_FRATT | Q5NGF2 from UniProtKB/TrEMBL  Length:347

    Alignment length:348
                             1                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339        
         Q5NGF2_FRATT     - -MAGLKYEDAGVNIEAGNQAVERMKQHVKKTFTQDVLTGLGSFGSLYSLKNIINNYDDPVLVQSIDGVGTKTKVAVMCGKFENLGYDLFSAATNDIVVMGAKPITFLDYVAHDKLDPAIMEELVKGMSKACAECGVSLVGGETAEMPGVYQAGEIDMVGVITGIVDRKRIINGENIKEGDIVFGLSSSGLHTNGYSFARKLFFDVAGNKHTDTYPELEGKTIGDVLLEPHINYTNIIHDFLDNGVDIKGMAHITGGGFIENIPRVLPQGLGAQIDKDSFATPAIFKLMQRIGDISEFEMYRSFNMGIGMTIIASQDQFDKMQELAKKHTNTKLYQIGKITNSGKVEII 347
               SCOP domains d3m84a1 A:0-170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                                          d3m84a2 A:171-347 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhh.....ee..hhhhh.eeehhhhhhhh..eeeeeeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeeeeeeeeee.hhh..........eeeeee.......hhhhhhhhhhh.........hhhhh..hhhhhhh.....hhhhhhhhhhh.....eeee...hhhhhhhhhhh....eeeee.hhh..hhhhhhhhhhhh.hhhhhhhhh...eeeeeeehhhhhhhhhhhhh......eeeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m84 A   0 AmAGLKYEDAGVNIEAGNQAVERmKQHVKKTFTQDVLTGLGSFGSLYSLKNIINNYDDPVLVQSIDGVGTKTKVAVmCGKFENLGYDLFSAATNDIVVmGAKPITFLDYVAHDKLDPAImEELVKGmSKACAECGVSLVGGETAEmPGVYQAGEIDmVGVITGIVDRKRIINGENIKEGDIVFGLSSSGLHTNGYSFARKLFFDVAGNKHTDTYPELEGKTIGDVLLEPHINYTNIIHDFLDNGVDIKGmAHITGGGFIENIPRVLPQGLGAQIDKDSFATPAIFKLmQRIGDISEFEmYRSFNmGIGmTIIASQDQFDKmQELAKKHTNTKLYQIGKITNSGKVEII 347
                             |       9        19   |    29        39        49        59        69      | 79        89        99       109       119      |129       139     | 149      |159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    |  309       319|      329       339        
                             |                    23-MSE                                               76-MSE                98-MSE              119-MSE  |                145-MSE    156-MSE                                                                                      249-MSE                               287-MSE    298-MSE |   |         320-MSE                       
                             1-MSE                                                                                                                      126-MSE                                                                                                                                                                           304-MSE                                       
                                                                                                                                                                                                                                                                                                                                              308-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with Q5NGF2_FRATT | Q5NGF2 from UniProtKB/TrEMBL  Length:347

    Alignment length:350
                               1                                                                                                                                                                                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347
         Q5NGF2_FRATT     - ---MAGLKYEDAGVNIEAGNQAVERMKQHVKKTFTQDVLTGLGSFGSLYSLKNIINNYDDPVLVQSIDGVGTKTKVAVMCGKFENLGYDLFSAATNDIVVMGAKPITFLDYVAHDKLDPAIMEELVKGMSKACAECGVSLVGGETAEMPGVYQAGEIDMVGVITGIVDRKRIINGENIKEGDIVFGLSSSGLHTNGYSFARKLFFDVAGNKHTDTYPELEGKTIGDVLLEPHINYTNIIHDFLDNGVDIKGMAHITGGGFIENIPRVLPQGLGAQIDKDSFATPAIFKLMQRIGDISEFEMYRSFNMGIGMTIIASQDQFDKMQELAKKHTNTKLYQIGKITNSGKVEII 347
               SCOP domains d3m84b1 B:-2-170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                                           d3m84b2 B:171-347 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------AIRS-3m84B01 B:16-142                                                                                                          ---------------------------------AIRS_C-3m84B03 B:176-347                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) ------------------AIRS-3m84B02 B:16-142                                                                                                          ---------------------------------AIRS_C-3m84B04 B:176-347                                                                                                                                                     Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhhh.....eee......eeeehhhhhh....eeeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeeeeeeeeee.hhh..........eeeeee.......hhhhhhhhhhh.........hhhhh..hhhhhhhh....hhhhhhhhhhh.....eeee...hhhhhhhhhhh....eeeee.hhh..hhhhhhhhhhhh.hhhhhhhhh...eeeeeeehhhhhhhhhhhhh......eeeeeeee....eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m84 B  -2 SNAmAGLKYEDAGVNIEAGNQAVERmKQHVKKTFTQDVLTGLGSFGSLYSLKNIINNYDDPVLVQSIDGVGTKTKVAVmCGKFENLGYDLFSAATNDIVVmGAKPITFLDYVAHDKLDPAImEELVKGmSKACAECGVSLVGGETAEmPGVYQAGEIDmVGVITGIVDRKRIINGENIKEGDIVFGLSSSGLHTNGYSFARKLFFDVAGNKHTDTYPELEGKTIGDVLLEPHINYTNIIHDFLDNGVDIKGmAHITGGGFIENIPRVLPQGLGAQIDKDSFATPAIFKLmQRIGDISEFEmYRSFNmGIGmTIIASQDQFDKmQELAKKHTNTKLYQIGKITNSGKVEII 347
                               |     7        17     |  27        37        47        57        67        77        87        97|      107       117 |     127       137       147       157       167       177       187       197       207       217       227       237       247 |     257       267       277       287       297|     |307|      317  |    327       337       347
                               1-MSE                23-MSE                                               76-MSE                98-MSE              119-MSE  |                145-MSE    156-MSE                                                                                      249-MSE                               287-MSE    298-MSE |   |         320-MSE                       
                                                                                                                                                          126-MSE                                                                                                                                                                           304-MSE                                       
                                                                                                                                                                                                                                                                                                                                                308-MSE
   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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M84)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5NGF2_FRATT | Q5NGF2)
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: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:0004641    phosphoribosylformylglycinamidine cyclo-ligase activity    Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + 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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        Q5NGF2_FRATT | Q5NGF2: 3qty

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