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(-) Description

Title :  MIRAS PHASING OF THE AQUIFEX AEOLICUS PPX/GPPA PHOSPHATASE: CRYSTAL STRUCTURE OF THE TYPE II VARIANT
 
Authors :  O. Kristensen, M. Laurberg, A. Liljas, J. S. Kastrup, M. Gajhede
Date :  06 May 04  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Protein, Actin-Like Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kristensen, M. Laurberg, A. Liljas, J. S. Kastrup, M. Gajhede
Structural Characterization Of The Stringent Response Related Exopolyphosphatase/Guanosine Pentaphosphate Phosphohydrolase Protein Family
Biochemistry V. 43 8894 2004
PubMed-ID: 15248747  |  Reference-DOI: 10.1021/BI049083C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXOPOLYPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.11, 3.6.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPX
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: PPX/GPPA PHOSPHATASE

 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CSX2Mod. Amino AcidS-OXY CYSTEINE
3MSE8Mod. Amino AcidSELENOMETHIONINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CSX1Mod. Amino AcidS-OXY CYSTEINE
3MSE4Mod. Amino AcidSELENOMETHIONINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CSX1Mod. Amino AcidS-OXY CYSTEINE
3MSE4Mod. Amino AcidSELENOMETHIONINE
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:142 , GLY B:143 , GLY B:145 , SER B:146 , ILE B:167 , HOH B:527BINDING SITE FOR RESIDUE CL B 501
2AC2SOFTWAREGLN A:142 , GLY A:143 , GLY A:145 , GLY A:166 , ILE A:167BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREGLU A:38 , TYR A:226 , PRO A:228 , ASP A:294 , ARG A:298 , GLU A:299 , HOH A:660BINDING SITE FOR RESIDUE TRS A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:178 -Pro A:179
2Tyr A:224 -Pro A:225
3Asp B:178 -Pro B:179
4Tyr B:224 -Pro B:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6D)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6D)

(-) 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:303
 aligned with O67040_AQUAE | O67040 from UniProtKB/TrEMBL  Length:312

    Alignment length:303
                                    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   
         O67040_AQUAE     8 IMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEVLKEN 310
               SCOP domains d1t6da1 A:8-132 Exopolyphosphatase Ppx                                                                                       d1t6da2 A:133-310 Exopolyphosphatase Ppx                                                                                                                                           SCOP domains
               CATH domains 1t6dA01 A:8-131  [code=3.30.420.40, no name defined]                                                                        1t6dA02 A:132-310 Exopolyphosphatase. Domain 2                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeeee....eeeeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee..eeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhh.....hhhhhh..eeehhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t6d A   8 ImRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERmKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVmVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDcLIVSDWGLREGVLVSEmLKEN 310
                             |      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   
                             |                                                                       82-MSE                                                 138-MSE                                                                                                                                                289-CSX          306-MSE
                             9-MSE                                                                                                                                                                                                                                                                                                         


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

    Alignment length:300
                                    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
         O67040_AQUAE     8 IMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEVL 307
               SCOP domains d1t6db1 B:8-132 Exopolyphosphatase Ppx                                                                                       d1t6db2 B:133-307 Exopolyphosphatase Ppx                                                                                                                                        SCOP domains
               CATH domains 1t6dB01 B:8-131  [code=3.30.420.40, no name defined]                                                                        1t6dB02 B:132-307 Exopolyphosphatase. Domain 2                                                                                                                                   CATH domains
           Pfam domains (1) ----------------Ppx-GppA-1t6dB01 B:24-307                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ----------------Ppx-GppA-1t6dB02 B:24-307                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ..eeeeeee...eeeeeeeee....eeeeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhh.....hhhhhh..eeehhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6d B   8 ImRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERmKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVmVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDcLIVSDWGLREGVLVSEmL 307
                             |      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
                             9-MSE                                                                   82-MSE                                                 138-MSE                                                                                                                                                289-CSX          306-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) 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 2j4r

(-) Related Entries Specified in the PDB File

1t6c THE SAME PROTEIN IN WILD TYPE AT RESOLUTION 1.53 A