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(-) Description

Title :  PHOSPHORIBOSYLAMINE-GLYCINE LIGASE FROM YERSINIA PESTIS
 
Authors :  J. Osipiuk, M. Zhou, L. Papazisi, W. F. Anderson, A. Joachimiak
Date :  12 Apr 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Phosphoribosylamine-Glycine Ligase, Center For Structural Genomics Of Infectious Diseases, Csgid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, L. Papazisi, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of Phosphoribosylamine-Glycine Ligase From Yersinia Pestis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINE--GLYCINE LIGASE
    Chains: A
    EC Number: 6.3.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURD, Y0501, YPO3729, YP_3092
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: GARS, GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 23)

Asymmetric/Biological Unit (8, 23)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE11Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7PGE1Ligand/IonTRIETHYLENE GLYCOL
8SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:193 , GLU A:194 , GLN A:213 , ASP A:214 , HIS A:215 , ASP A:222 , TYR A:421 , ARG A:422 , HOH A:589BINDING SITE FOR RESIDUE GOL A 501
02AC2SOFTWAREGLN A:398 , LYS A:417 , HOH A:441 , HOH A:668BINDING SITE FOR RESIDUE GOL A 502
03AC3SOFTWARELYS A:27 , SER A:62 , HIS A:63 , GLN A:96 , ALA A:97 , GLN A:100 , ASN A:264 , HOH A:675 , HOH A:860BINDING SITE FOR RESIDUE PGE A 504
04AC4SOFTWAREGLU A:162 , GLU A:165 , THR A:166 , ASN A:169 , ASP A:170BINDING SITE FOR RESIDUE PEG A 505
05AC5SOFTWAREALA A:210 , ARG A:302 , TRP A:326 , SO4 A:509 , HOH A:796BINDING SITE FOR RESIDUE EDO A 506
06AC6SOFTWAREGLN A:409 , CYS A:415 , LYS A:417 , HOH A:429 , HOH A:740BINDING SITE FOR RESIDUE BME A 507
07AC7SOFTWAREARG A:383 , HOH A:432 , HOH A:433 , HOH A:838 , HOH A:916 , HOH A:927BINDING SITE FOR RESIDUE SO4 A 508
08AC8SOFTWAREALA A:210 , THR A:211 , EDO A:506 , HOH A:576 , HOH A:696 , HOH A:782BINDING SITE FOR RESIDUE SO4 A 509
09AC9SOFTWAREILE A:48 , ALA A:261 , GLU A:262 , GLY A:263 , HOH A:490 , HOH A:742 , HOH A:793BINDING SITE FOR RESIDUE SO4 A 510
10BC1SOFTWAREGLY A:152 , LYS A:153 , GLY A:154 , VAL A:155 , HOH A:836BINDING SITE FOR RESIDUE SO4 A 511
11BC2SOFTWARESER A:104 , LYS A:105 , ALA A:106 , HOH A:907 , HOH A:908BINDING SITE FOR RESIDUE SO4 A 512
12BC3SOFTWAREASP A:214 , LYS A:216 , GLY A:228 , ARG A:290 , ASP A:293 , PRO A:294 , GLU A:295BINDING SITE FOR RESIDUE NA A 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Pro A:32
2Ala A:140 -Pro A:141
3Ser A:234 -Pro A:235
4Asp A:293 -Pro A:294
5Tyr A:341 -Pro A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARSPS00184 Phosphoribosylglycinamide synthetase signature.PUR2_YERPE290-297  1A:290-297

(-) Exons   (0, 0)

(no "Exon" information available for 3MJF)

(-) 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:429
 aligned with PUR2_YERPE | Q8ZAR2 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:429
                             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       349       359       369       379       389       399       409       419         
           PUR2_YERPE     - -MNILIIGNGGREHALGWKAAQSPLADKIYVAPGNAGTALEPTLENVDIAATDIAGLLAFAQSHDIGLTIVGPEAPLVIGVVDAFRAAGLAIFGPTQAAAQLEGSKAFTKDFLARHNIPSAEYQNFTDVEAALAYVRQKGAPIVIKADGLAAGKGVIVAMTQEEAETAVNDMLAGNAFGDAGHRIVVEEFLDGEEASFIVMVDGENVLPMATSQDHKRVGDGDTGPNTGGMGAYSPAPVVTDDVHQRVMDQVIWPTVRGMAAEGNIYTGFLYAGLMISADGQPKVIEFNCRFGDPETQPIMLRMRSDLVELCLAGTQGKLNEKTSDWDERPSLGVVLAAGGYPADYRQGDVIHGLPQQEVKDGKVFHAGTKLNGNHEVVTNGGRVLCVTALGETVAQAQQYAYQLAEGIQWEGVFCRKDIGYRAIARGK 428
               SCOP domains d3mjfa1 A:0-103 automated matches                                                                       d3mjfa2 A:104-327 automated matches                                                                                                                                                                                             d3mjfa3 A:328-428 automated matches                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -GARS_N-3mjfA03 A:1-102                                                                                GARS_A-3mjfA01 A:103-296                                                                                                                                                                          ---------------------------------GARS_C-3mjfA02 A:330-424                                                                       ---- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhh....eeeeeeee.hhhhhhh...ee......hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhh....eeeee....eeeeeeeeee...eee....ee..eee...eeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....eeeeee.hhhh..hhhhhhhhh..hhhhhhhhhhh.hhhhh........eeeeeeee.......................eeeee..eee.....eee...eeeeeeee..hhhhhhhhhhhhhh......ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjf A   0 AmNILIIGNGGREHALGWKAAQSPLADKIYVAPGNAGTALEPTLENVDIAATDIAGLLAFAQSHDIGLTIVGPEAPLVIGVVDAFRAAGLAIFGPTQAAAQLEGSKAFTKDFLARHNIPSAEYQNFTDVEAALAYVRQKGAPIVIKADGLAAGKGVIVAmTQEEAETAVNDmLAGNAFGDAGHRIVVEEFLDGEEASFIVmVDGENVLPmATSQDHKRVGDGDTGPNTGGmGAYSPAPVVTDDVHQRVmDQVIWPTVRGmAAEGNIYTGFLYAGLmISADGQPKVIEFNCRFGDPETQPImLRmRSDLVELCLAGTQGKLNEKTSDWDERPSLGVVLAAGGYPADYRQGDVIHGLPQQEVKDGKVFHAGTKLNGNHEVVTNGGRVLCVTALGETVAQAQQYAYQLAEGIQWEGVFCRKDIGYRAIARGK 428
                             |       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       349       359       369       379       389       399       409       419         
                             |                                                                                                                                                           159-MSE     171-MSE                      200-MSE  209-MSE              230-MSE           248-MSE    259-MSE         275-MSE                  300-MSE                                                                                                                            
                             1-MSE                                                                                                                                                                                                                                                                                                       303-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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
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 3MJF)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: GARS_C] (12)
(-)
Clan: no clan defined [family: GARS_N] (12)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR2_YERPE | Q8ZAR2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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:0004637    phosphoribosylamine-glycine ligase activity    Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + 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:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    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.

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