2XG8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURAL BASIS OF GENE REGULATION BY PROTEIN PII: THE CRYSTAL COMPLEX OF PII AND PIPX FROM SYNECHOCOCCUS ELONGATUS PCC 7942

Authors :   J. L. Llacer, V. Rubio

Date :   01 Jun 10 (Deposition) - 18 Aug 10 (Release) - 15 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Transcription, Pii Signaling Protein, Ntca Co-Activator Protein Pipx, Tudor-Like Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Llacer, J. Espinosa, M. A. Castells, A. Contreras, K. Forchhammer, V. Rubio
Structural Basis For The Regulation Of Ntca- Dependent Transcription By Proteins Pipx And Pii.
Proc. Natl. Acad. Sci. Usa V. 107 15397 2010
PubMed-ID: 20716687 | Reference-DOI: 10.1073/PNAS.1007015107

Molecule 1 - NITROGEN REGULATORY PROTEIN P-II
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942
	Synonym	:	PII SIGNAL TRANSDUCING PROTEIN

Molecule 2 - PIPX
	Chains	:	D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2XG8)

(no "Site" information available for 2XG8)

(no "SS Bond" information available for 2XG8)

Asymmetric Unit

No.	Residues
1	Arg A:38	-	Gln A:39
2	Gly A:48	-	Ser A:49
3	Phe B:36	-	Gly B:37
4	Arg B:38	-	Gln B:39
5	Gln B:39	-	Lys B:40
6	Gly B:48	-	Ser B:49
7	Arg C:38	-	Gln C:39
8	Gln C:39	-	Lys C:40
9	Gly C:41	-	Gln C:42
10	Gln C:42	-	Thr C:43
11	Thr C:43	-	Glu C:44
12	Gly C:48	-	Ser C:49
13	Phe D:21	-	Gly D:22
14	Gly D:22	-	Asp D:23
15	Asp D:23	-	Ser D:24
16	Gln D:34	-	Arg D:35
17	Asp D:43	-	Ala D:44
18	Arg D:45	-	Gly D:46
19	Phe E:21	-	Gly E:22
20	Gly E:22	-	Asp E:23
21	Asp E:23	-	Ser E:24
22	Gln E:34	-	Arg E:35
23	Asp E:43	-	Ala E:44
24	Ala E:44	-	Arg E:45
25	Ser E:73	-	Leu E:74
26	Leu E:74	-	Gln E:75
27	Gly F:22	-	Asp F:23
28	Gln F:34	-	Arg F:35
29	Asp F:43	-	Ala F:44
30	Ala F:44	-	Arg F:45

(no "SAP(SNP)/Variant" information available for 2XG8)

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNE7	1-112	3	A:1-110 B:1-108 C:1-112
2	PII_GLNB_UMP	PS00496	P-II protein uridylation site.	GLNB_SYNE7	46-51	3	A:46-51 B:46-51 C:46-51
3	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNE7	83-96	3	A:83-96 B:83-96 C:83-96

Biological Unit 1 (3, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PII_GLNB_DOM	PS51343	P-II protein family profile.	GLNB_SYNE7	1-112	6	A:1-110 B:1-108 C:1-112
2	PII_GLNB_UMP	PS00496	P-II protein uridylation site.	GLNB_SYNE7	46-51	6	A:46-51 B:46-51 C:46-51
3	PII_GLNB_CTER	PS00638	P-II protein C-terminal region signature.	GLNB_SYNE7	83-96	6	A:83-96 B:83-96 C:83-96

(no "Exon" information available for 2XG8)

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:106
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNAD 110
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xg8A00 A:1-110  [code=3.30.70.120, no     name defined]                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee...----ee....eeee..eeeeeeeeee...hhhhhhhhhhhhhh......eeeeeee..eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: A:1-110 UniProt: 1-112                                                                      PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER -------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2xg8 A   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQ----ERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNAD 110
                                    10        20        30        |-   |    50        60        70        80        90       100       110
                                                                 39   44

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2xg8B00 B:1-108  [code=3.30.70.120, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.......ee....eeee..eeeeeeeeee...hhhhhhhhhhhhhh......eeeeeee.eeeeee..eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: B:1-108 UniProt: 1-112                                                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2xg8 B   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI 112
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xg8C00 C:1-112  [code=3.30.70.120, no name defined]                                                             CATH domains
           Pfam domains (1) ---P-II-2xg8C01 C:4-105                                                                                  ------- Pfam domains (1)
           Pfam domains (2) ---P-II-2xg8C02 C:4-105                                                                                  ------- Pfam domains (2)
           Pfam domains (3) ---P-II-2xg8C03 C:4-105                                                                                  ------- Pfam domains (3)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh....eeeeeeeee.......ee....eeee..eeeeeeeeee...hhhhhhhhhhhhhh......eeeeeee.eeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: C:1-112 UniProt: 1-112                                                                        PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2xg8 C   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI 112
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:87
 aligned with Q7X386_SYNE7 | Q7X386 from UniProtKB/TrEMBL  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
         Q7X386_SYNE7     3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeeee.....eeeee..ee..eeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2xg8 D   3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
                                    12        22        32        42        52        62        72        82

Chain E from PDB  Type:PROTEIN  Length:87
 aligned with Q7X386_SYNE7 | Q7X386 from UniProtKB/TrEMBL  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
         Q7X386_SYNE7     3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeeee.....eeeee..ee..eeeeee....eeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2xg8 E   3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
                                    12        22        32        42        52        62        72        82

Chain F from PDB  Type:PROTEIN  Length:78
 aligned with Q7X386_SYNE7 | Q7X386 from UniProtKB/TrEMBL  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
         Q7X386_SYNE7     3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF3539-2xg8F01 F:3-89                                                                  Pfam domains (1)
           Pfam domains (2) DUF3539-2xg8F02 F:3-89                                                                  Pfam domains (2)
           Pfam domains (3) DUF3539-2xg8F03 F:3-89                                                                  Pfam domains (3)
         Sec.struct. author ...eeee...eeeeeeee.....eeeee..ee..eeeee......e-eeehhhhhhhhhhhhhhhhh.--------hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2xg8 F   3 SENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTR-EPIGRNEARMLVDNRLRQLRR--------QLQQVFKQTFL  89
                                    12        22        32        42     | |52        62       | -      | 82       
                                                                        48 |                  70       79          
                                                                          50

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 '\|'

(no "SCOP Domain" information available for 2XG8)

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)

Synechococcus elongatus. Organism_taxid: 1140. Strain: pcc 7942. (4)

1a	2xg8A00	A:1-110
1b	2xg8B00	B:1-108
1c	2xg8C00	C:1-112

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (GLNB_SYNE7 | P0A3F4)

molecular function
	GO:0030234	enzyme regulator activity	Binds to and modulates the activity of an enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.

Chain D,E,F (Q7X386_SYNE7 | Q7X386)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2xg8)

	Sites
(no "Sites" information available for 2xg8)

	Cis Peptide Bonds
		Ala E:44 - Arg E:45	[ RasMol ]
		Ala F:44 - Arg F:45	[ RasMol ]
		Arg A:38 - Gln A:39	[ RasMol ]
		Arg B:38 - Gln B:39	[ RasMol ]
		Arg C:38 - Gln C:39	[ RasMol ]
		Arg D:45 - Gly D:46	[ RasMol ]
		Asp D:23 - Ser D:24	[ RasMol ]
		Asp D:43 - Ala D:44	[ RasMol ]
		Asp E:23 - Ser E:24	[ RasMol ]
		Asp E:43 - Ala E:44	[ RasMol ]
		Asp F:43 - Ala F:44	[ RasMol ]
		Gln B:39 - Lys B:40	[ RasMol ]
		Gln C:39 - Lys C:40	[ RasMol ]
		Gln C:42 - Thr C:43	[ RasMol ]
		Gln D:34 - Arg D:35	[ RasMol ]
		Gln E:34 - Arg E:35	[ RasMol ]
		Gln F:34 - Arg F:35	[ RasMol ]
		Gly A:48 - Ser A:49	[ RasMol ]
		Gly B:48 - Ser B:49	[ RasMol ]
		Gly C:41 - Gln C:42	[ RasMol ]
		Gly C:48 - Ser C:49	[ RasMol ]
		Gly D:22 - Asp D:23	[ RasMol ]
		Gly E:22 - Asp E:23	[ RasMol ]
		Gly F:22 - Asp F:23	[ RasMol ]
		Leu E:74 - Gln E:75	[ RasMol ]
		Phe B:36 - Gly B:37	[ RasMol ]
		Phe D:21 - Gly D:22	[ RasMol ]
		Phe E:21 - Gly E:22	[ RasMol ]
		Ser E:73 - Leu E:74	[ RasMol ]
		Thr C:43 - Glu C:44	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2xg8
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	Q7X386_SYNE7 \| Q7X386
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	GLNB_SYNE7 \| P0A3F4
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	Q7X386_SYNE7 \| Q7X386
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UniProtKB/Swiss-Prot
	GLNB_SYNE7 \| P0A3F4	:	1qy7 2jj4 2v5h 2xbp 2xul 2xzw 4aff 4c3k 4c3l 4c3m
UniProtKB/TrEMBL
	Q7X386_SYNE7 \| Q7X386	:	2xko

1qy7	THE STRUCTURE OF THE PII PROTEIN FROM THE CYANOBACTERIASYNECHOCOCCUS SP. PCC 7942
2jj4	THE COMPLEX OF PII AND ACETYLGLUTAMATE KINASE FROM SYNECHOCOCCUS ELONGATUS PCC7942
2v5h	CONTROLLING THE STORAGE OF NITROGEN AS ARGININE: THE COMPLEX OF PII AND ACETYLGLUTAMATE KINASE FROM SYNECHOCOCCUS ELONGATUS PCC 7942
2xbp	A NOVEL SIGNAL TRANSDUCTION PROTEIN PII VARIANT FROM SYNECHOCOCCUS ELONGATUS PCC7942 INDICATES A TWO-STEP PROCESS FOR NAGK PII COMPLEX FORMATION
2xko	CRYSTAL STRUCTURE OF THE COMPLEX OF NTCA WITH ITS TRANSCRIPTIONAL CO-ACTIVATOR PIPX

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (30, 30)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 9)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 3)

Pfam Domains (2, 6)

Gene Ontology (8, 8)

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