1QMP - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   PHOSPHORYLATED ASPARTATE IN THE CRYSTAL STRUCTURE OF THE SPORULATION RESPONSE REGULATOR, SPO0A

Authors :   R. J. Lewis, J. A. Brannigan, K. Muchova, I. Barak, A. J. Wilkinson

Date :   04 Oct 99 (Deposition) - 14 Nov 99 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Replication, Response Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Lewis, J. A. Brannigan, K. Muchova, I. Barak, A. J. Wilkinson
Phosphorylated Aspartate In The Structure Of A Response Regulator Protein
J. Mol. Biol. V. 294 9 1999
PubMed-ID: 10556024 | Reference-DOI: 10.1006/JMBI.1999.3261

Molecule 1 - SPO0A
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Taxid	:	469008
	Fragment	:	RECEIVER DOMAIN
	Organism Scientific	:	BACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Other Details	:	PHOSPHORYLATED ASPARTIC ACID RESIDUE 55

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	PHD	4	Mod. Amino Acid	ASPARTYL PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PHD	1	Mod. Amino Acid	ASPARTYL PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PHD	1	Mod. Amino Acid	ASPARTYL PHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PHD	1	Mod. Amino Acid	ASPARTYL PHOSPHATE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PHD	1	Mod. Amino Acid	ASPARTYL PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , PHD A:55 , ILE A:57 , HOH A:404 , HOH A:413 , HOH B:425	BINDING SITE FOR RESIDUE CA W 301
2	AC2	SOFTWARE	ASP B:10 , PHD B:55 , ILE B:57 , HOH B:403 , HOH B:419 , HOH C:437	BINDING SITE FOR RESIDUE CA X 301
3	AC3	SOFTWARE	ASP C:10 , PHD C:55 , ILE C:57 , HOH D:437 , HOH D:428 , HOH D:415	BINDING SITE FOR RESIDUE CA Y 301
4	AC4	SOFTWARE	HOH A:457 , ASP D:10 , PHD D:55 , ILE D:57 , HOH D:402 , HOH D:412	BINDING SITE FOR RESIDUE CA Z 301

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

Asymmetric Unit

No.	Residues
1	Lys A:106	-	Pro A:107
2	Lys B:106	-	Pro B:107
3	Lys C:106	-	Pro C:107
4	Lys D:106	-	Pro D:107

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	SP0A_GEOSE	4-121	4	A:4-121 B:4-121 C:4-121 D:4-121

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	SP0A_GEOSE	4-121	1	A:4-121 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	SP0A_GEOSE	4-121	1	- B:4-121 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	SP0A_GEOSE	4-121	1	- - C:4-121 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	SP0A_GEOSE	4-121	1	- - - D:4-121

(no "Exon" information available for 1QMP)

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:126
 aligned with SP0A_GEOSE | P52934 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SP0A_GEOSE     2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
               SCOP domains d1qmpa_ A: Sporulation response regulator Spo0A                                                                                 SCOP domains
               CATH domains 1qmpA00 A:2-128  [code=3.40.50.2300, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.-.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: A:4-121 UniProt: 4-121                                                                      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmp A   2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLdIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK-TPVV 128
                                    11        21        31        41        51   |    61        71        81        91       101       111       121 | |   
                                                                                55-PHD                                                             123 |   
                                                                                                                                                     125

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with SP0A_GEOSE | P52934 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SP0A_GEOSE     2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
               SCOP domains d1qmpb_ B: Sporulation response regulator Spo0A                                                                                 SCOP domains
               CATH domains 1qmpB00 B:2-128  [code=3.40.50.2300, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhh----..eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh--.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: B:4-121 UniProt: 4-121                                                                      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmp B   2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLdIIMPHLDGLAVLERIRA----QPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYG--TPVV 128
                                    11        21        31        41        51   |    61        71|    |  81        91       101       111       121|  |   
                                                                                55-PHD           72   77                                          122  |   
                                                                                                                                                     125

Chain C from PDB  Type:PROTEIN  Length:126
 aligned with SP0A_GEOSE | P52934 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SP0A_GEOSE     2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
               SCOP domains d1qmpc_ C: Sporulation response regulator Spo0A                                                                                 SCOP domains
               CATH domains 1qmpC00 C:2-128  [code=3.40.50.2300, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.-.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: C:4-121 UniProt: 4-121                                                                      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmp C   2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLdIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK-TPVV 128
                                    11        21        31        41        51   |    61        71        81        91       101       111       121 | |   
                                                                                55-PHD                                                             123 |   
                                                                                                                                                     125

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with SP0A_GEOSE | P52934 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SP0A_GEOSE     2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
               SCOP domains d1qmpd_ D: Sporulation response regulator Spo0A                                                                                 SCOP domains
               CATH domains 1qmpD00 D:2-128  [code=3.40.50.2300, no name defined]                                                                           CATH domains
           Pfam domains (1) ---Response_reg-1qmpD01 D:5-118                                                                                      ---------- Pfam domains (1)
           Pfam domains (2) ---Response_reg-1qmpD02 D:5-118                                                                                      ---------- Pfam domains (2)
           Pfam domains (3) ---Response_reg-1qmpD03 D:5-118                                                                                      ---------- Pfam domains (3)
           Pfam domains (4) ---Response_reg-1qmpD04 D:5-118                                                                                      ---------- Pfam domains (4)
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhh.--...eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: D:4-121 UniProt: 4-121                                                                      ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmp D   2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLdIIMPHLDGLAVLERIRAG--HQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTTPVV 128
                                    11        21        31        41        51   |    61        71 |  |   81        91       101       111       121       
                                                                                55-PHD            73 76

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: CheY-related (166)

Protein domain: Sporulation response regulator Spo0A (2)

Bacillus stearothermophilus [TaxId: 1422] (2)

1a	d1qmpa_	A:
1b	d1qmpb_	B:
1c	d1qmpc_	C:
1d	d1qmpd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Bacillus stearothermophilus. Organism_taxid: 1422. (1)

1a	1qmpA00	A:2-128
1b	1qmpC00	C:2-128
1c	1qmpD00	D:2-128
1d	1qmpB00	B:2-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (1)

1a	Response_reg-1qmpD01	D:5-118
1b	Response_reg-1qmpD02	D:5-118
1c	Response_reg-1qmpD03	D:5-118
1d	Response_reg-1qmpD04	D:5-118

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SP0A_GEOSE | P52934)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0051606	detection of stimulus	The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
	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:0043937	regulation of sporulation	Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
	GO:0042173	regulation of sporulation resulting in formation of a cellular spore	Any process that modulates the frequency, rate or extent of spore formation.
	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.
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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	1qmp
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(no "Related Entries Specified in the PDB File" available for 1QMP)

Description

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Ligands, Modified Residues, Ions (2, 8)

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