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(-) Description

Title :  CRYSTAL STRUCTURE OF RAPH COMPLEXED WITH SPO0F
 
Authors :  V. Parashar, M. B. Neiditch
Date :  16 Dec 10  (Deposition) - 23 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (2x)
Biol. Unit 2:  B,D  (2x)
Keywords :  Tetratricopeptide Repeat, 3-Helix Bundle, Phosphorelay Signal Transduction, Phosphatase, Response Regulator Receiver, Hydrolase- Kinase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Parashar, N. Mirouze, D. A. Dubnau, M. B. Neiditch
Structural Basis Of Response Regulator Dephosphorylation By Rap Phosphatases.
Plos Biol. V. 9 E1000 2011
PubMed-ID: 21346797  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000589

(-) Compounds

Molecule 1 - RESPONSE REGULATOR ASPARTATE PHOSPHATASE H
    ChainsA, B
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneBSU06830, RAPH, YEEH, YZQA
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymPSP28
 
Molecule 2 - SPORULATION INITIATION PHOSPHOTRANSFERASE F
    ChainsC, D
    EC Number2.7.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneBSU37130, SPO0F
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymSTAGE 0 SPORULATION PROTEIN F

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)A C 
Biological Unit 2 (2x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:153 , GLN A:154 , THR A:155 , PHE A:193 , LEU A:368 , GLU A:371 , HOH A:453 , HOH A:466BINDING SITE FOR RESIDUE GOL A 377
2AC2SOFTWARELYS A:144 , ARG A:178BINDING SITE FOR RESIDUE SO4 A 378
3AC3SOFTWARELYS B:153 , GLN B:154 , THR B:155 , LEU B:368 , GLU B:371 , HOH B:389BINDING SITE FOR RESIDUE GOL B 377
4AC4SOFTWAREARG B:178BINDING SITE FOR RESIDUE SO4 B 378
5AC5SOFTWAREASP C:11 , ASP C:54 , LYS C:56BINDING SITE FOR RESIDUE MG C 125
6AC6SOFTWAREASP D:11 , ASP D:54 , LYS D:56BINDING SITE FOR RESIDUE MG D 125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q15)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys C:104 -Pro C:105
2Lys D:104 -Pro D:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q15)

(-) PROSITE Motifs  (3, 12)

Asymmetric Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.SP0F_BACSU5-119
 
  2C:5-119
D:5-119
2TPRPS50005 TPR repeat profile.RAPH_BACSU99-132
 
139-172
 
180-213
 
220-253
 
  8A:99-132
B:99-132
A:139-172
B:139-172
A:180-213
B:180-213
A:220-253
B:220-253
3TPR_REGIONPS50293 TPR repeat region circular profile.RAPH_BACSU99-253
 
  2A:99-253
B:99-253
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.SP0F_BACSU5-119
 
  2C:5-119
-
2TPRPS50005 TPR repeat profile.RAPH_BACSU99-132
 
139-172
 
180-213
 
220-253
 
  8A:99-132
-
A:139-172
-
A:180-213
-
A:220-253
-
3TPR_REGIONPS50293 TPR repeat region circular profile.RAPH_BACSU99-253
 
  2A:99-253
-
Biological Unit 2 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.SP0F_BACSU5-119
 
  2-
D:5-119
2TPRPS50005 TPR repeat profile.RAPH_BACSU99-132
 
139-172
 
180-213
 
220-253
 
  8-
B:99-132
-
B:139-172
-
B:180-213
-
B:220-253
3TPR_REGIONPS50293 TPR repeat region circular profile.RAPH_BACSU99-253
 
  2-
B:99-253

(-) Exons   (0, 0)

(no "Exon" information available for 3Q15)

(-) 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:365
 aligned with RAPH_BACSU | Q59HN8 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
           RAPH_BACSU     4 AIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDILKGECLYAY 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..--------.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------TPR  PDB: A:99-132 UniProt: 99-132---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------TPR_REGION  PDB: A:99-253 UniProt: 99-253                                                                                                                  --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------TPR  PDB: A:139-172               -------TPR  PDB: A:180-213               ------TPR  PDB: A:220-253               --------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q15 A   4 AIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLE--------PTVTELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDILKGECLYAY 376
                                    13        23        33        43        53        63    |    -   |    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
                                                                                           68       77                                                                                                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:332
 aligned with RAPH_BACSU | Q59HN8 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
           RAPH_BACSU     4 AIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDILKGECLYAY 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------TPR_2-3q15B03 B:99-131           ----------------------------------------TPR_12-3q15B01 B:172-252                                                         ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------TPR_2-3q15B04 B:99-131           ----------------------------------------TPR_12-3q15B02 B:172-252                                                         ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....-------------------hhhhhhhhhhhhhhhhhhhhh-------------------.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------TPR  PDB: B:99-132 UniProt: 99-132---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------TPR_REGION  PDB: B:99-253 UniProt: 99-253                                                                                                                  --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------TPR  PDB: B:139-172               -------TPR  PDB: B:180-213               ------TPR  PDB: B:220-253               --------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q15 B   4 AIPSSRVGVKINEWYKMIRQFSV-------------------DQDLLIYYSLMCFRHQLMLDY-------------------IETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITA---KFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDILKGECLYAY 376
                                    13        23  |      -         -  |     53        63  |      -         -  |     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       | - |     303       313       323       333       343       353       363       373   
                                                 26                  46                  66                  86                                                                                                                                                                                                          291 295                                                                                 

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with SP0F_BACSU | P06628 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:116
                                    13        23        33        43        53        63        73        83        93       103       113      
           SP0F_BACSU     4 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 119
               SCOP domains d3q15c_ C: Sporulation response regulator Spo0F                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh....eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: C:5-119 UniProt: 5-119                                                                    PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3q15 C   4 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 119
                                    13        23        33        43        53        63        73        83        93       103       113      

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with SP0F_BACSU | P06628 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:116
                                    13        23        33        43        53        63        73        83        93       103       113      
           SP0F_BACSU     4 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 119
               SCOP domains d3q15d_ D: Sporulation response regulator Spo0F                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Response_reg-3q15D01 D:6-116                                                                                   --- Pfam domains (1)
           Pfam domains (2) --Response_reg-3q15D02 D:6-116                                                                                   --- Pfam domains (2)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhh...eeeeee----------------..eee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: D:5-119 UniProt: 5-119                                                                    PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3q15 D   4 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMT----------------LTHFAKPFDIDEIRDAVKKYL 119
                                    13        23        33        43        53        63        73        |-         -     | 103       113      
                                                                                                         82               99                    

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q15)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: CheY (97)
(-)
Clan: TPR (230)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RAPH_BACSU | Q59HN8)
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:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
biological process
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.

Chain C,D   (SP0F_BACSU | P06628)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3q15
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 Related Entries

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

UniProtKB/Swiss-Prot
        SP0F_BACSU | P066281f51 1fsp 1nat 1pey 1pux 1srr 2fsp 2ftk 2jvi 2jvj 2jvk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3Q15)