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(-) Description

Title :  CRYSTAL STRUCTURES OF THE ADP AND ATP BOUND FORMS OF THE BACILLUS ANTI-SIGMA FACTOR SPOIIAB IN COMPLEX WITH THE ANTI-ANTI-SIGMA SPOIIAA:POISED FOR PHOSPHORYLATION COMPLEX WITH ATP, CRYSTAL FORM II
 
Authors :  S. Masuda, K. S. Murakami, S. Wang, C. A. Olson, J. Donigan, F. Leon, S. A. Darst, E. A. Campbell
Date :  02 Jun 04  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F  (2x)
Keywords :  Spoiiab, Spoiia, Anti-Sigma, Anti-Anti-Sigma, Sporulation, Serine Kinasea, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Masuda, K. S. Murakami, S. Wang, C. A. Olson, J. Donigian, F. Leon, S. A. Darst, E. A. Campbell
Crystal Structures Of The Adp And Atp Bound Forms Of The Bacillus Anti-Sigma Factor Spoiiab In Complex With The Anti-Anti-Sigma Spoiiaa.
J. Mol. Biol. V. 340 941 2004
PubMed-ID: 15236958  |  Reference-DOI: 10.1016/J.JMB.2004.05.040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-SIGMA F FACTOR
    ChainsA, C, E
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSPOIIAB
    MutationYES
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymSTAGE II SPORULATION PROTEIN AB
 
Molecule 2 - ANTI-SIGMA F FACTOR ANTAGONIST
    ChainsB, D, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSPOIIAA
    MutationYES
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymSTAGE II SPORULATION PROTEIN AA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABCD  
Biological Unit 2 (2x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:46 , ASN A:50 , ATP A:200BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWAREGLU C:46 , ASN C:50 , ATP C:201BINDING SITE FOR RESIDUE MG C 301
3AC3SOFTWAREGLU E:46 , ASN E:50 , GLY E:109 , ATP E:202BINDING SITE FOR RESIDUE MG E 302
4AC4SOFTWAREGLU A:46 , ASN A:50 , ALA A:51 , HIS A:54 , GLY A:55 , ASP A:81 , GLY A:85 , ILE A:86 , ALA A:92 , THR A:98 , THR A:99 , ARG A:105 , SER A:106 , GLY A:107 , MET A:108 , GLY A:109 , PHE A:110 , THR A:130 , MG A:300 , HOH A:301 , HOH A:305 , HOH A:316 , HOH A:320 , ALA B:58BINDING SITE FOR RESIDUE ATP A 200
5AC5SOFTWAREGLU C:46 , ASN C:50 , HIS C:54 , GLY C:55 , ASP C:81 , GLY C:85 , ILE C:86 , ALA C:92 , THR C:98 , THR C:99 , ARG C:105 , SER C:106 , GLY C:107 , MET C:108 , GLY C:109 , PHE C:110 , THR C:130 , MG C:301 , HOH C:308 , HOH C:315 , HOH C:329 , ALA D:58BINDING SITE FOR RESIDUE ATP C 201
6AC6SOFTWAREGLU E:46 , ASN E:50 , ALA E:51 , HIS E:54 , GLY E:55 , ASP E:81 , ILE E:86 , ALA E:92 , THR E:98 , THR E:99 , ARG E:105 , SER E:106 , GLY E:107 , MET E:108 , GLY E:109 , PHE E:110 , THR E:130 , MG E:302 , HOH E:318 , ALA F:58BINDING SITE FOR RESIDUE ATP E 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TIL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STASPS50801 STAS domain profile.SP2AA_GEOSE3-113
 
 
  3B:3-113
D:3-113
F:3-113
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STASPS50801 STAS domain profile.SP2AA_GEOSE3-113
 
 
  2B:3-113
D:3-113
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STASPS50801 STAS domain profile.SP2AA_GEOSE3-113
 
 
  2-
-
F:3-113

(-) Exons   (0, 0)

(no "Exon" information available for 1TIL)

(-) 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:141
 aligned with SP2AB_GEOSE | O32727 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
          SP2AB_GEOSE     1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTTDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKAYCEK 141
               SCOP domains d1tila_ A: Anti-sigma factor spoIIab                                                                                                          SCOP domains
               CATH domains 1tilA00 A:1-141  [code=3.30.565.10, no name defined]                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeee......hhhhhh......hhhhh...hhhhhhhhhh.eeeeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1til A   1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTMDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKHIVKS 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with SP2AA_GEOSE | O32726 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:117
                             1                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       
          SP2AA_GEOSE     - -MSLAIDLEVKQDELIVRLSGELDHHTAENCMNKCRMCLEKRAIRHIVLNLGQLTFMDSSGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
               SCOP domains d1tilb_ B: Anti-sigma factor antagonist SpoIIaa                                                                       SCOP domains
               CATH domains 1tilB00 B:0-116  [code=3.30.750.24, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeehhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh.....eee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---STAS  PDB: B:3-113 UniProt: 3-113                                                                              --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1til B   0 HMSLAIDLEVKQDVLIVRLSGELDHHTAEELREQVTDVLENRAIRHIVLNLGQLTFMDASGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
                                     9        19        29        39        49        59        69        79        89        99       109       

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with SP2AB_GEOSE | O32727 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
          SP2AB_GEOSE     1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTTDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKAYCEK 141
               SCOP domains d1tilc_ C: Anti-sigma factor spoIIab                                                                                                          SCOP domains
               CATH domains 1tilC00 C:1-141  [code=3.30.565.10, no name defined]                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeee......hhhhhh......hhhhh...hhhhhhhhhh.eeeeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1til C   1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTMDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKHIVKS 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with SP2AA_GEOSE | O32726 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:118
                              1                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108        
          SP2AA_GEOSE     - --MSLAIDLEVKQDELIVRLSGELDHHTAENCMNKCRMCLEKRAIRHIVLNLGQLTFMDSSGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
               SCOP domains d1tild_ D: Anti-sigma factor antagonist SpoIIaa                                                                        SCOP domains
               CATH domains 1tilD00 D:-1-116  [code=3.30.750.24, no name defined]                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeehhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhheee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----STAS  PDB: D:3-113 UniProt: 3-113                                                                              --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1til D  -1 SHMSLAIDLEVKQDVLIVRLSGELDHHTAEELREQVTDVLENRAIRHIVLNLGQLTFMDASGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
                                     8        18        28        38        48        58        68        78        88        98       108        

Chain E from PDB  Type:PROTEIN  Length:140
 aligned with SP2AB_GEOSE | O32727 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          SP2AB_GEOSE     1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTTDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKAYCE 140
               SCOP domains d1tile_ E: Anti-sigma factor spoIIab                                                                                                         SCOP domains
               CATH domains 1tilE00 E:1-140  [code=3.30.565.10, no name defined]                                                                                         CATH domains
           Pfam domains (1) ----------------------------------HATPase_c-1tilE01 E:35-136                                                                            ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------HATPase_c-1tilE02 E:35-136                                                                            ---- Pfam domains (2)
           Pfam domains (3) ----------------------------------HATPase_c-1tilE03 E:35-136                                                                            ---- Pfam domains (3)
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeee......hhhhhh......hhhhh...hhhhhhhhhh.eeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1til E   1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTMDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKHIVK 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain F from PDB  Type:PROTEIN  Length:117
 aligned with SP2AA_GEOSE | O32726 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:117
                             1                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       
          SP2AA_GEOSE     - -MSLAIDLEVKQDELIVRLSGELDHHTAENCMNKCRMCLEKRAIRHIVLNLGQLTFMDSSGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
               SCOP domains d1tilf_ F: Anti-sigma factor antagonist SpoIIaa                                                                       SCOP domains
               CATH domains 1tilF00 F:0-116  [code=3.30.750.24, no name defined]                                                                  CATH domains
           Pfam domains (1) ----STAS-1tilF01 F:4-109                                                                                      ------- Pfam domains (1)
           Pfam domains (2) ----STAS-1tilF02 F:4-109                                                                                      ------- Pfam domains (2)
           Pfam domains (3) ----STAS-1tilF03 F:4-109                                                                                      ------- Pfam domains (3)
         Sec.struct. author ...eeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeehhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhheee.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---STAS  PDB: F:3-113 UniProt: 3-113                                                                              --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1til F   0 HMSLAIDLEVKQDVLIVRLSGELDHHTAEELREQVTDVLENRAIRHIVLNLGQLTFMDASGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFDMSGLFKIIRVEADEQFALQALGVA 116
                                     9        19        29        39        49        59        69        79        89        99       109       

   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, 6)

Asymmetric Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: STAS (15)

(-) Gene Ontology  (16, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E   (SP2AB_GEOSE | O32727)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016989    sigma factor antagonist activity    The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
    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:0030436    asexual sporulation    The formation of spores derived from the products of an asexual cell division. Examples of this process are found in bacteria and fungi.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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.

Chain B,D,F   (SP2AA_GEOSE | O32726)
molecular function
    GO:0045152    antisigma factor binding    Interacting selectively and non-covalently with an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator.
    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).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SP2AA_GEOSE | O327261th8 1thn 1tid
        SP2AB_GEOSE | O327271l0o 1th8 1thn 1tid

(-) Related Entries Specified in the PDB File

1th8 INHIBITORY COMPLEX, CRYSTAL FOR II
1thn INHIBITORY COMPLEX, CRYSTAL FORM I
1tid POISED FOR PHOSPHORYLATION COMPLEX , CRYSTAL FORM I