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(-) Description

Title :  CRYSTAL STRUCTURE OF GMP SYNTHETASE PH1347 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  S. Maruoka, S. Horita, W. C. Lee, K. Nagata, M. Tanokura
Date :  07 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp Pyrophosphatase, Glutamine Amidotransferase, Gmp Synthetase, Purine Nucleotide Biosynthesis, Atp-Binding, Gmp Biosynthesis, Ligase, Nucleotide-Binding, Purine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Maruoka, S. Horita, W. C. Lee, K. Nagata, M. Tanokura
Crystal Structure Of The Atppase Subunit And Its Substrate-Dependent Association With The Gatase Subunit: A Novel Regulatory Mechanism For A Two-Subunit-Type Gmp Synthetase From Pyrococcus Horikoshii Ot3.
J. Mol. Biol. V. 395 417 2010
PubMed-ID: 19900465  |  Reference-DOI: 10.1016/J.JMB.2009.10.053

(-) Compounds

Molecule 1 - GMP SYNTHASE [GLUTAMINE-HYDROLYZING] SUBUNIT B
    Chains: A, B
    EC Number: 6.3.5.2
    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: GUAAB, PH1347
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3
    Synonym: ATPPASE SUBUNIT, GMP SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3A4I)

(-) Sites  (0, 0)

(no "Site" information available for 3A4I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A4I)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:130 -Pro A:131
2Lys A:300 -Pro A:301
3Pro A:301 -Pro A:302
4Ala B:130 -Pro B:131
5Lys B:300 -Pro B:301
6Pro B:301 -Pro B:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A4I)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GMPS_ATP_PPASEPS51553 GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile.GUAAB_PYRHO1-185
 		  2A:1-185
B:1-185

(-) Exons   (0, 0)

(no "Exon" information available for 3A4I)

(-) 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:286
 aligned with GUAAB_PYRHO | O59072 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
          GUAAB_PYRHO     1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAPDWIESQGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
               SCOP domains d3a4ia1 A:1-189 automated matches                                                                                                                                                            d3a4ia2 A:190-308 automated matches                                                                                     SCOP domains
               CATH domains 3a4iA01 A:1-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                    3a4iA02 A:186-308  [code=3.30.300.10, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.....eeeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eee......----------------------..eee......hhhhhhhhhhhh..hhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeee..eeeeeeeeeeeeee.......ee...hhhhhhhhhhhhhhhh..eeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GMPS_ATP_PPASE  PDB: A:1-185 UniProt: 1-185                                                                                                                                              --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4i A   1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAP----------------------NLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -         -   |   160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                                                                            131                    154                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with GUAAB_PYRHO | O59072 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
          GUAAB_PYRHO     1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAPDWIESQGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
               SCOP domains d3a4ib1 B:1-189 automated matches                                                                                                                                                            d3a4ib2 B:190-308 automated matches                                                                                     SCOP domains
               CATH domains 3a4iB01 B:1-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                    3a4iB02 B:186-308  [code=3.30.300.10, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eee......----------------------..eee......hhhhhhhhhhhh..hhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee................eeeeeeeeee.....eee...hhhhhhhhhhhhhhhh..eeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GMPS_ATP_PPASE  PDB: B:1-185 UniProt: 1-185                                                                                                                                              --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4i B   1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAP----------------------NLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -         -   |   160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                                                                            131                    154
   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)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A4I)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GUAAB_PYRHO | O59072)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003922    GMP synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: ATP + xanthosine 5'-phosphate + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate.
    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:0016462    pyrophosphatase activity    Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
biological process
    GO:0006177    GMP biosynthetic process    The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
    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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  Cis Peptide Bonds
    Ala A:130 - Pro A:131   [ RasMol ]  
    Ala B:130 - Pro B:131   [ RasMol ]  
    Lys A:300 - Pro A:301   [ RasMol ]  
    Lys B:300 - Pro B:301   [ RasMol ]  
    Pro A:301 - Pro A:302   [ RasMol ]  
    Pro B:301 - Pro B:302   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GUAAB_PYRHO | O59072: 2dpl

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