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(-) Description

Title :  HIGH-RESOLUTION STRUCTURE OF THE DING PROTEIN FROM PSEUDOMONAS FLUORESCENS
 
Authors :  S. Moniot, S. Ahn, M. Elias, D. Kim, K. Scott, E. Chabriere
Date :  14 Jun 07  (Deposition) - 17 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A
Keywords :  Ding Protein, Phosphate-Binding, Venus Flytrap Fold, Psts Protein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahn, S. Moniot, M. Elias, E. Chabriere, D. Kim, K. Scott
Structure-Function Relationships In A Bacterial Ding Protein.
Febs Lett. V. 581 3455 2007
PubMed-ID: 17612529  |  Reference-DOI: 10.1016/J.FEBSLET.2007.06.050

(-) Compounds

Molecule 1 - DING
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Strain: SBW 25

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4PO41Ligand/IonPHOSPHATE ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:7 , THR A:8 , LEU A:9 , GLY A:31 , SER A:32 , ASP A:62 , ARG A:141 , SER A:145 , GLY A:146 , THR A:147BINDING SITE FOR RESIDUE PO4 A 901
02AC2SOFTWARELYS A:158 , HOH A:1146 , HOH A:1448 , HOH A:1451BINDING SITE FOR RESIDUE ACT A 902
03AC3SOFTWARETHR A:169 , THR A:170 , HOH A:964 , HOH A:1188 , HOH A:1218 , HOH A:1395 , HOH A:1646BINDING SITE FOR RESIDUE ACT A 904
04AC4SOFTWARETHR A:169 , THR A:174 , THR A:338 , HOH A:1188 , HOH A:1218 , HOH A:1587 , HOH A:1601BINDING SITE FOR RESIDUE SO4 A 908
05AC5SOFTWAREMET A:0 , ASP A:1 , LYS A:54 , HOH A:963 , HOH A:1457 , HOH A:1492BINDING SITE FOR RESIDUE SO4 A 911
06AC6SOFTWAREALA A:302 , PRO A:369 , LEU A:370 , HOH A:1093 , HOH A:1121 , HOH A:1144 , HOH A:1160 , HOH A:1178BINDING SITE FOR RESIDUE EDO A 903
07AC7SOFTWAREALA A:186 , HOH A:1228BINDING SITE FOR RESIDUE EDO A 906
08AC8SOFTWARELEU A:180 , ALA A:182 , ALA A:244 , HOH A:1578 , HOH A:1670BINDING SITE FOR RESIDUE EDO A 907
09AC9SOFTWAREARG A:345 , HOH A:968 , HOH A:1008 , HOH A:1075 , HOH A:1572 , HOH A:1588BINDING SITE FOR RESIDUE EDO A 909
10BC1SOFTWAREASP A:107 , ARG A:227 , GLN A:237 , HOH A:1440BINDING SITE FOR RESIDUE EDO A 910
11BC2SOFTWAREPHE A:98 , ASN A:99 , LYS A:224 , HOH A:995 , HOH A:1064 , HOH A:1265 , HOH A:1545BINDING SITE FOR RESIDUE GOL A 905

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:114 -A:159
2A:300 -A:363

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q9T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q9T)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q9T)

(-) 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:374
 aligned with D0VWY2_PSEFS | D0VWY2 from UniProtKB/TrEMBL  Length:379

    Alignment length:374
                                    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       310       320       330       340       350       360       370    
         D0VWY2_PSEFS     1 MDINGGGATLPQALYQTSGVLTAGFAQYIGVGSGNGKAAFLNNDYTKFQAGVTNKNVHWAGSDSKLSATELSTYASAKQPTWGKLIQVPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTWDGISGSGRTGPIVVVYRSESSGTTELFTRFLNAKCNAETGNFAVTTTFGTSFSGGLPAGAVAATGSQGVMTALAAGDGRITYMSPDFAAPTLAGLDDATKVARVGKNVATNTQGVSPAAANVSAAIGAVPVPAAADRSNPDAWVPVFGPDNTAGVQPYPTSGYPILGFTNLIFSQCYADATQTTQVRDFFTKHYGASNNNDAAITANAFVPLPTAWKATVRASFLTASNALSIGNTNVCNGIGRPLLEH 374
               SCOP domains d2q9ta_ A: Phosphate-binding protein                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -PBP_like_2-2q9tA01 A:1-320                                                                                                                                                                                                                                                                                                      ----------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhh............ee.hhhhhhhhhhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhh.eeeeeeeeee....ee.......eehhhhhhhhhhh...hhhhh.........eeeee...hhhhhhhhhhhhhhh...........hhhhh.........eeehhhhhhhhhhhh...ee..........hhhhhhh.....ee.............hhhhhhhhhhh....hhhhh.hhhhhh..ee.......ee........eeeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9t A   0 MDINGGGATLPQALYQTSGVLTAGFAQYIGVGSGNGKAAFLNNDYTKFQAGVTNKNVHWAGSDSKLSATELSTYASAKQPTWGKLIQVPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTWDGISGSGRTGPIVVVYRSESSGTTELFTRFLNAKCNAETGNFAVTTTFGTSFSGGLPAGAVAATGSQGVMTALAAGDGRITYMSPDFAAPTLAGLDDATKVARVGKNVATNTQGVSPAAANVSAAIGAVPVPAAADRSNPDAWVPVFGPDNTAGVQPYPTSGYPILGFTNLIFSQCYADATQTTQVRDFFTKHYGASNNNDAAITANAFVPLPTAWKATVRASFLTASNALSIGNTNVCNGIGRPLLEH 373
                                     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    


Chain A from PDB  Type:PROTEIN  Length:374
 aligned with Q4KD17_PSEF5 | Q4KD17 from UniProtKB/TrEMBL  Length:392

    Alignment length:381
                                                                                                                                                                                           184                                                                                                                                                                                                                           
                                                                                                                                                                                         183 |                                                                251      252                                                                                                                                         392   
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 |     192       202       212       222       232       242        |-       254       264       274       284       294       304       314       324       334       344       354       364       374       384       | - 
         Q4KD17_PSEF5    24 ADINGGGATLPQPLYQTAGVLTAGFAPYIGVGSGNGKAAFLNNDYTKFVAGTTGKNVHWAGSDSKLSAAELKGYEDNHQAAWGKLIQVPSVATSVAVPFNKAGSTAVDLSVNDLCGVFSGRVSKWEQLPTSGRTGAITVVYRNESSGTTELFTRFLNAKC-AETGTFAVTTNFASSYSGGLPAGAVAAVTSQGVMDALNAGDGRITYMSPDYAAPTLAGLDDATKVAKV--------AGVSPAPANVSSAIAAVAVPDTTVRGDQNLWVPVFTSQANIDANPSDKSLRLYPTSGYPILGFTNLIFSQCYADANQTSQVRAFFSRHYGALVNNDTAINNNRFVPLPAAWKTAVRDSFVTASSGLSIGNASVCNAIGRPL---   -
               SCOP domains d2q9ta_ A: Phosphate-binding protein                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -PBP_like_2-2q9tA01 A:1-320                                                                                                                                                                                                                                                               -------                                       ----------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhh............ee.hhhhhhhhhhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhh.eeeeeeeeee....ee.......eehhhhhhhhhhh...hhhhh.........eeeee...hhhhhhhhhhhhhhh...........hhhhh.........eeehhhhhhhhhhhh...ee..........hhhhhhh.....ee.............hhhhhhhhhhh....hhhhh.hhhhhh..ee.......ee-------........eeeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9t A   0 MDINGGGATLPQALYQTSGVLTAGFAQYIGVGSGNGKAAFLNNDYTKFQAGVTNKNVHWAGSDSKLSATELSTYASAKQPTWGKLIQVPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTWDGISGSGRTGPIVVVYRSESSGTTELFTRFLNAKCNAETGNFAVTTTFGTSFSGGLPAGAVAATGSQGVMTALAAGDGRITYMSPDFAAPTLAGLDDATKVARVGKNVATNTQGVSPAAANVSAAIGAVPVPAAADRSNPDAWVPVFGPDNTAGVQP-------YPTSGYPILGFTNLIFSQCYADATQTTQVRDFFTKHYGASNNNDAAITANAFVPLPTAWKATVRASFLTASNALSIGNTNVCNGIGRPLLEH 373
                                     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 |     282       292       302       312       322       332       342       352       362       372 
                                                                                                                                                                                                                                                                                                                   281     282
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q9T)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4KD17_PSEF5 | Q4KD17)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042301    phosphate ion binding    Interacting selectively and non-covalently with phosphate.
biological process
    GO:0035435    phosphate ion transmembrane transport    The directed movement of phosphate across a membrane by means of some agent such as a transporter or pore.
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.

Chain A   (D0VWY2_PSEFS | D0VWY2)
molecular function
    GO:0042301    phosphate ion binding    Interacting selectively and non-covalently with phosphate.
biological process
    GO:0035435    phosphate ion transmembrane transport    The directed movement of phosphate across a membrane by means of some agent such as a transporter or pore.
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.

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  2q9t
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 Related Entries

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