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(-) Description

Title :  STRUCTURAL STUDY OF THE AQUIFEX AEOLICUS PPX-GPPA ENZYME
 
Authors :  O. Kristensen
Date :  05 Sep 06  (Deposition) - 16 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ppgpp, Aquifex Aeolicus, Stringent Response, Hydrolase, Exopolyphosphatase, Guanosine Pentaphosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kristensen, B. Ross, M. Gajhede
Structure Of The Ppx/Gppa Phosphatase From Aquifex Aeolicus In Complex With The Alarmone Ppgpp
J. Mol. Biol. V. 375 1469 2008
PubMed-ID: 18155044  |  Reference-DOI: 10.1016/J.JMB.2007.11.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXOPOLYPHOSPHATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-A
    Expression System Taxid: 562
    Fragment: RESIDUES 7-310
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: GUANOSINE PENTAPHOSPHATE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1G4P1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1G4P1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1G4P-1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , SER A:18 , ASN A:19 , SER A:20 , ARG A:22 , ILE A:42 , THR A:87 , GLN A:142 , GLU A:159 , GLY A:211 , ARG A:266 , ARG A:267 , HOH A:2070 , HOH A:2079BINDING SITE FOR RESIDUE G4P A1307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J4R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:178 -Pro A:179
2Asp B:178 -Pro B:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J4R)

(-) Exons   (0, 0)

(no "Exon" information available for 2J4R)

(-) Sequences/Alignments

Asymmetric 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:300
 aligned with O67040_AQUAE | O67040 from UniProtKB/TrEMBL  Length:312

    Alignment length:300
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
         O67040_AQUAE     7 PIMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEV 306
               SCOP domains d2j4ra1 A:7-132 automated matches                                                                                             d2j4ra2 A:133-306 automated matches                                                                                                                                            SCOP domains
               CATH domains 2j4rA01 A:7-131  [code=3.30.420.40, no name defined]                                                                         2j4rA02 A:132-306 Exopolyphosphatase. Domain 2                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeee....eeeeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh.....eeeeee....eeeeeee..eeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhh.............eeehhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j4r A   7 PIMRVASIDIGSNSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEV 306
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with O67040_AQUAE | O67040 from UniProtKB/TrEMBL  Length:312

    Alignment length:300
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
         O67040_AQUAE     7 PIMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEV 306
               SCOP domains d2j4rb1 B:7-132 automated matches                                                                                             d2j4rb2 B:133-306 automated matches                                                                                                                                            SCOP domains
               CATH domains 2j4rB01 B:7-131  [code=3.30.420.40, no name defined]                                                                         2j4rB02 B:132-306 Exopolyphosphatase. Domain 2                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeee..eeeeeeeeeee.............hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhh....eeeeee....eeeeeee..eeeeeeee....hhhhhhhh.....hhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhh....hhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j4r B   7 PIMRVASIDIGSNSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEV 306
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
   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  (1, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J4R)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O67040_AQUAE | O67040)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        O67040_AQUAE | O67040: 1t6c 1t6d

(-) Related Entries Specified in the PDB File

1t6c STRUCTURAL CHARACTERIZATION OF THE PPX/GPPA PROTEIN FAMILY:CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS FAMILY MEMBER
1t6d MIRAS PHASING OF THE AQUIFEX AEOLICUS PPX/ GPPA PHOSPHATASE:CRYSTAL STRUCTURE OF THE TYPE II VARIANT