1UL3 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PII FROM SYNECHOCYSTIS SP. PCC 6803

Authors :   Y. Xu, P. D. Carr, P. Clancy, M. Garcia-Dominguez, K. Forchhammer, F. Fl N. Tandeau De Marsac, S. G. Vasudevan, D. L. Ollis

Date :   09 Sep 03 (Deposition) - 16 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Nitrogen Regulation, Cyanobacteria, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Xu, P. D. Carr, P. Clancy, M. Garcia-Dominguez, K. Forchhammer, F. Florencio, S. G. Vasudevan, N. Tandeau De Marsac, D. L. Ollis
The Structures Of The Pii Proteins From The Cyanobacteria Synechococcus Sp. Pcc 7942 And Synechocystis Sp. Pcc 6803.
Acta Crystallogr. , Sect. D V. 59 2183 2003
PubMed-ID: 14646076 | Reference-DOI: 10.1107/S0907444903019589

Molecule 1 - NITROGEN REGULATORY PROTEIN P-II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMAB11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	GLNB
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1143
	Synonym	:	PII SIGNAL TRANSDUCING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:11 , ASP A:14 , GLU A:15 , PHE C:11 , ASP C:14 , GLU C:15	BINDING SITE FOR RESIDUE CA C 601
2	AC2	SOFTWARE	PHE B:11 , ASP B:14 , GLU B:15 , PHE D:11 , ASP D:14 , GLU D:15	BINDING SITE FOR RESIDUE CA B 602
3	AC3	SOFTWARE	PHE A:36 , LYS A:58 , GLY A:89 , LYS A:90 , HOH A:525 , HOH A:526 , MET C:28	BINDING SITE FOR RESIDUE GOL A 500
4	AC4	SOFTWARE	LYS A:90 , PHE A:92 , VAL C:26 , GLY C:27 , ILE C:63 , VAL C:64 , HOH C:627	BINDING SITE FOR RESIDUE GOL C 501

(no "SS Bond" information available for 1UL3)

(no "Cis Peptide Bond" information available for 1UL3)

(no "SAP(SNP)/Variant" information available for 1UL3)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNY3	1-112	4	A:1-112 B:1-112 C:1-112 D:1-110
2	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNY3	83-96	4	A:83-96 B:83-96 C:83-96 D:83-96

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNY3	1-112	3	A:1-112 B:1-112 C:1-112 -
2	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNY3	83-96	3	A:83-96 B:83-96 C:83-96 -

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNY3	1-112	3	- - - D:1-110
2	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNY3	83-96	3	- - - D:83-96

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNY3	1-112	4	A:1-112 B:1-112 C:1-112 D:1-110
2	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNY3	83-96	4	A:83-96 B:83-96 C:83-96 D:83-96

(no "Exon" information available for 1UL3)

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:95
 aligned with GLNB_SYNY3 | Q55247 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           GLNB_SYNY3     1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
               SCOP domains d1ul3a_ A: PII (product of glnB)                                                                                 SCOP domains
               CATH domains 1ul3A00 A:1-112  [code=3.30.70.120,                  no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh.....eeeeeeee.-----------------..eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: A:1-112 UniProt: 1-112                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------PII_GLNB_CTER ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1ul3 A   1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGF-----------------EFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
                                    10        20        30     |   -         -   |    60        70        80        90       100       110  
                                                              36                54

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with GLNB_SYNY3 | Q55247 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           GLNB_SYNY3     1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
               SCOP domains d1ul3b_ B: PII (product of glnB)                                                                                 SCOP domains
               CATH domains 1ul3B00 B:1-112  [code=3.30.70.120,                   no name defined]                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh.....eeeeeeeee------------------.eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: B:1-112 UniProt: 1-112                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------PII_GLNB_CTER ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1ul3 B   1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGF------------------FLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
                                    10        20        30     |   -         -    |   60        70        80        90       100       110  
                                                              36                 55

Chain C from PDB  Type:PROTEIN  Length:94
 aligned with GLNB_SYNY3 | Q55247 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           GLNB_SYNY3     1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
               SCOP domains d1ul3c_ C: PII (product of glnB)                                                                                 SCOP domains
               CATH domains 1ul3C00 C:1-112  [code=3.30.70.120,                   no name defined]                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh.....eeeeeeee------------------.eeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee..eeee....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: C:1-112 UniProt: 1-112                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------PII_GLNB_CTER ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1ul3 C   1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGF------------------FLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTEAI 112
                                    10        20        30     |   -         -    |   60        70        80        90       100       110  
                                                              36                 55

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with GLNB_SYNY3 | Q55247 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
           GLNB_SYNY3     1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTE 110
               SCOP domains d1ul3d_ D: PII (product of glnB)                                                                               SCOP domains
               CATH domains 1ul3D00 D:1-110  [code=3.30.70.120, no                name defined]                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh.....eeeeeeee..---------------.eeeeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeee...ee......ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: D:1-110 UniProt: 1-112                                                                      PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------PII_GLNB_CTER -------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1ul3 D   1 MKKVEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGR---------------EFLQKLKIEIVVDEGQVDMVVDKLVSAARTGEIGDGKIFISPVDSVVRIRTGEKDTE 110
                                    10        20        30       | -         -   |    60        70        80        90       100       110
                                                                38              54

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: GlnB-like (79)

Family: Prokaryotic signal transducing protein (31)

Protein domain: PII (product of glnB) (17)

Cyanobacteria (Synechococcus sp.) pcc pcc 6803 [TaxId: 1131] (1)

1a	d1ul3a_	A:
1b	d1ul3b_	B:
1c	d1ul3c_	C:
1d	d1ul3d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.120, no name defined] (37)

Synechocystis sp.. Organism_taxid: 1143. (1)

1a	1ul3A00	A:1-112
1b	1ul3D00	D:1-110
1c	1ul3B00	B:1-112
1d	1ul3C00	C:1-112

(no "Pfam Domain" information available for 1UL3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GLNB_SYNY3 | Q55247)

molecular function
	GO:0030234	enzyme regulator activity	Binds to and modulates the activity of an enzyme.
	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).
biological process
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0006808	regulation of nitrogen utilization	Any process that modulates the frequency, rate or extent of nitrogen utilization.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	1ul3
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	GLNB_SYNY3 \| Q55247
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1hwu	SAME PROTEIN FROM HERBASPIRILLUM SEROPEDICAE
2pii	SAME PROTEIN FROM E.COLI

Description

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Ligands, Modified Residues, Ions (2, 4)

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