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Title :   CRYSTAL STRUCTURE OF SIGNAL RECEIVER DOMAIN OF MODULATED DIGUANYLATE CYCLASE FROM DESULFOVIBRIO DESULFURICANS G20, AN EXAMPLE OF ALTERNATE FOLDING

Authors :   Y. Patskovsky, J. B. Bonanno, R. Romero, M. Gilmore, S. Chang, C. Grosho J. Koss, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New Yor Research Center For Structural Genomics (Nysgxrc)

Date :   04 Mar 08 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Signal Receiver Domain, Diguanylate Cyclase, Protein Structure Initiative, Psi-2, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, J. B. Bonanno, R. Romero, M. Gilmore, S. Chang, C. Groshong, J. Koss, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Signal Receiver Domain Of Modulated Diguanylate Cyclase From Desulfovibrio Desulfuricans.
To Be Published
PubMed: search

Molecule 1 - RESPONSE REGULATOR RECEIVER MODULATED DIGUANYLATE CYCLASE WITH PAS/PAC SENSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Taxid	:	562
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Gene	:	DDE_1631
	Organism Scientific	:	DESULFOVIBRIO DESULFURICANS SUBSP. DESULFURICANS STR.
	Organism Taxid	:	207559
	Strain	:	G20

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3CG0)

(no "Site" information available for 3CG0)

(no "SS Bond" information available for 3CG0)

Asymmetric Unit

No.	Residues
1	Lys A:109	-	Pro A:110
2	Lys B:109	-	Pro B:110
3	Lys C:109	-	Pro C:110
4	Lys D:109	-	Pro D:110

(no "SAP(SNP)/Variant" information available for 3CG0)

(no "PROSITE Motif" information available for 3CG0)

(no "Exon" information available for 3CG0)

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 Q311G8_DESAG | Q311G8 from UniProtKB/TrEMBL  Length:561

    Alignment length:126
                                    15        25        35        45        55        65        75        85        95       105       115       125      
         Q311G8_DESAG     6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEQ 131
               SCOP domains d3cg0a_ A: automated matches                                                                                                   SCOP domains
               CATH domains 3cg0A00 A:6-131  [code=3.40.50.2300, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cg0 A   6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEE 131
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with Q311G8_DESAG | Q311G8 from UniProtKB/TrEMBL  Length:561

    Alignment length:125
                                    16        26        36        46        56        66        76        86        96       106       116       126     
         Q311G8_DESAG     7 LPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEQ 131
               SCOP domains d3cg0b_ B: automated matches                                                                                                  SCOP domains
               CATH domains 3cg0B00 B:7-131  [code=3.40.50.2300, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh......eeeee.......hhhhhhhhhhhhh...eeeeee..hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cg0 B   7 LPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEE 131
                                    16        26        36        46        56        66        76        86        96       106       116       126

Chain C from PDB  Type:PROTEIN  Length:126
 aligned with Q311G8_DESAG | Q311G8 from UniProtKB/TrEMBL  Length:561

    Alignment length:126
                                    15        25        35        45        55        65        75        85        95       105       115       125      
         Q311G8_DESAG     6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEQ 131
               SCOP domains d3cg0c_ C: automated matches                                                                                                   SCOP domains
               CATH domains 3cg0C00 C:6-131  [code=3.40.50.2300, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cg0 C   6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEE 131
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain D from PDB  Type:PROTEIN  Length:126
 aligned with Q311G8_DESAG | Q311G8 from UniProtKB/TrEMBL  Length:561

    Alignment length:126
                                    15        25        35        45        55        65        75        85        95       105       115       125      
         Q311G8_DESAG     6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEQ 131
               SCOP domains d3cg0d_ D: automated matches                                                                                                   SCOP domains
               CATH domains 3cg0D00 D:6-131  [code=3.40.50.2300, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cg0 D   6 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEE 131
                                    15        25        35        45        55        65        75        85        95       105       115       125

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(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: automated matches (82)

Protein domain: automated matches (82)

Desulfovibrio desulfuricans [TaxId: 207559] (1)

1a	d3cg0a_	A:
1b	d3cg0b_	B:
1c	d3cg0c_	C:
1d	d3cg0d_	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)

Desulfuricans str (Desulfovibrio desulfuricans subsp) (1)

1a	3cg0A00	A:6-131
1b	3cg0C00	C:6-131
1c	3cg0D00	D:6-131
1d	3cg0B00	B:7-131

(no "Pfam Domain" information available for 3CG0)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q311G8_DESAG | Q311G8)

molecular function
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	Cis Peptide Bonds
		Lys A:109 - Pro A:110	[ RasMol ]
		Lys B:109 - Pro B:110	[ RasMol ]
		Lys C:109 - Pro C:110	[ RasMol ]
		Lys D:109 - Pro D:110	[ RasMol ]

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