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Title :   CRYSTAL STRUCTURE OF THE BACILLUS STEAROTHERMOPHILUS ANTI-SIGMA FACTOR SPOIIAB WITH THE SPORULATION SIGMA FACTOR SIGMAF

Authors :   E. A. Campbell, S. Masuda, J. L. Sun, O. Muzzin, C. A. Olson, S. Wang, S. A. Darst

Date :   12 Feb 02 (Deposition) - 03 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Bergerat Fold, Helix-Turn-Helix, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Campbell, S. Masuda, J. L. Sun, O. Muzzin, C. A. Olson, S. Wang, S. A. Darst
Crystal Structure Of The Bacillus Stearothermophilus Anti-Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf.
Cell(Cambridge, Mass. ) V. 108 795 2002
PubMed-ID: 11955433 | Reference-DOI: 10.1016/S0092-8674(02)00662-1
(for further references see the PDB file header)

Molecule 1 - ANTI-SIGMA F FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SPOIIAB
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	SPOIIAB, STAGE II SPORULATION PROTEIN AB

Molecule 2 - SIGMA FACTOR
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 7-245
	Mutation	:	YES
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	SPOIIAC, SIGMA F

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:50 , HOH A:506 , ADP A:601	BINDING SITE FOR RESIDUE MG A 602
2	AC2	SOFTWARE	ASN B:50 , ADP B:701	BINDING SITE FOR RESIDUE MG B 702
3	AC3	SOFTWARE	ASN A:50 , ALA A:51 , HIS A:54 , GLY A:55 , ASP A:81 , ILE A:86 , ALA A:92 , PHE A:97 , THR A:98 , THR A:99 , ARG A:105 , SER A:106 , MET A:108 , GLY A:109 , PHE A:110 , THR A:130 , HOH A:502 , HOH A:506 , HOH A:528 , MG A:602	BINDING SITE FOR RESIDUE ADP A 601
4	AC4	SOFTWARE	ASN B:50 , ALA B:51 , HIS B:54 , GLY B:55 , ASP B:81 , GLY B:85 , ILE B:86 , ALA B:92 , PHE B:97 , THR B:98 , THR B:99 , GLY B:107 , MET B:108 , GLY B:109 , PHE B:110 , THR B:130 , HOH B:503 , HOH B:507 , HOH B:509 , HOH B:568 , MG B:702	BINDING SITE FOR RESIDUE ADP B 701

(no "SS Bond" information available for 1L0O)

(no "Cis Peptide Bond" information available for 1L0O)

(no "SAP(SNP)/Variant" information available for 1L0O)

(no "PROSITE Motif" information available for 1L0O)

(no "Exon" information available for 1L0O)

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)
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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 d1l0oa_ A: Anti-sigma factor spoIIab                                                                                                          SCOP domains
               CATH domains 1l0oA00 A:1-141  [code=3.30.565.10, no name defined]                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhheeeeeee...eeeeeeee......hhhhhhh.....hhhhh....hhhhhhhhh....eeee...eeee..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l0o 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: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 d1l0ob_ B: Anti-sigma factor spoIIab                                                                                                          SCOP domains
               CATH domains 1l0oB00 B:1-141  [code=3.30.565.10, no name defined]                                                                                          CATH domains
           Pfam domains (1) ----------------------------------HATPase_c-1l0oB01 B:35-136                                                                            ----- Pfam domains (1)
           Pfam domains (2) ----------------------------------HATPase_c-1l0oB02 B:35-136                                                                            ----- Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee...eee..eee......hhhhhh...............hhhhhhhhh......ee...eeee..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l0o B   1 MRNEMHLQFSARSENESFARVTVAAFVAQLDPTMDELTEIKTVVSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEARQPLFTTKPELERSGMGFTIMENFMDEVIVESEVNKGTTVYLKKHIVKS 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:57
 aligned with O32728_GEOSE | O32728 from UniProtKB/TrEMBL  Length:250

    Alignment length:57
                                   111       121       131       141       151       
         O32728_GEOSE   102 DGTVKVSRSLKEMGNKIRKAKDELSKTRGRSPTITEIADHLGISPEDVVLAQEAVRL 158
               SCOP domains d1l0oc_ C: SigmaF                                         SCOP domains
               CATH domains 1l0oC00 C:102-158                                         CATH domains
               Pfam domains -----------Sigma70_r3-1l0oC01 C:113-158                   Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1l0o C 102 DGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 158
                                   111       121       131       141       151

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Sigma70_r3 (4)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (1)

Sigma70_r3-1l0oC01

C:113-158

Clan: His_Kinase_A (147)

Family: HATPase_c (132)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (5)

2a	HATPase_c-1l0oB01	B:35-136
2b	HATPase_c-1l0oB02	B:35-136

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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 C (O32728_GEOSE | O32728)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0016987	sigma factor activity	A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	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.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
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