1VJ7 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CATALYTIC FRAGMENT OF RELSEQ, THE RELA/SPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS.

Authors :   T. Hogg, U. Mechold, H. Malke, M. Cashel, R. Hilgenfeld

Date :   03 Feb 04 (Deposition) - 04 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hd Domain, Alpha Beta 2-Layer Sandwich, Helix Bundle, Manganese, Gdp, Ppg2':3'P, (P)Ppgpp, Ppgpp, Rela, Spot, Stringent Response, Stringent Factor, Stringent Effector, Magic Spot, Rsh, Hydrolase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hogg, U. Mechold, H. Malke, M. Cashel, R. Hilgenfeld
Conformational Antagonism Between Opposing Active Sites In Bifunctional Rela/Spot Homolog Modulates (P)Ppgpp Metabolis During The Stringent Response.
Cell(Cambridge, Mass. ) V. 117 57 2004
PubMed-ID: 15066282 | Reference-DOI: 10.1016/S0092-8674(04)00260-0

Molecule 1 - BIFUNCTIONAL RELA/SPOT
	Chains	:	A, B
	EC Number	:	3.1.7.2, 2.7.6.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21(+)-PENH385
	Expression System Strain	:	BL21(LAMBDA DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	(P)PPGPP-3'-PYROPHOSPHOHYDROLASE AND (P)PPGPP-SYNTHETASE SUBDOMAINS
	Gene	:	RELA, REL, SPOT, RSH
	Organism Scientific	:	STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUISIMILIS
	Organism Taxid	:	119602
	Strain	:	SUBSP. EQUISIMILIS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GPX	1	Ligand/Ion	GUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE
3	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GPX	-1	Ligand/Ion	GUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GPX	1	Ligand/Ion	GUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , HIS A:77 , ASP A:144 , HOH A:2002 , HOH A:2089 , HOH A:2100	BINDING SITE FOR RESIDUE MN A 997
2	AC2	SOFTWARE	HIS B:53 , HIS B:77 , ASP B:78 , ASP B:144 , HOH B:2009 , HOH B:2178	BINDING SITE FOR RESIDUE MN B 1997
3	AC3	SOFTWARE	HIS A:176 , SER A:181 , TRP A:185 , ARG A:241 , LYS A:297 , TYR A:299 , LYS A:304 , ASN A:306 , TYR A:308 , HIS A:312 , GLN A:325 , ALA A:335 , HOH A:2022 , HOH A:2036 , HOH A:2153	BINDING SITE FOR RESIDUE GDP A 998
4	AC4	SOFTWARE	HIS B:176 , SER B:181 , TRP B:185 , ARG B:241 , LYS B:297 , TYR B:299 , LYS B:304 , ASN B:306 , TYR B:308 , HIS B:312 , GLU B:323 , GLN B:325 , ALA B:335	BINDING SITE FOR RESIDUE GDP B 1998
5	AC5	SOFTWARE	ARG B:44 , LYS B:45 , SER B:46 , ASN B:148 , THR B:151 , LEU B:155 , LYS B:159 , HOH B:2092 , HOH B:2104 , HOH B:2178 , HOH B:2231	BINDING SITE FOR RESIDUE GPX B 1999

(no "SS Bond" information available for 1VJ7)

(no "Cis Peptide Bond" information available for 1VJ7)

(no "SAP(SNP)/Variant" information available for 1VJ7)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	RELA_STREQ	50-149	2	A:50-149 B:50-149

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	RELA_STREQ	50-149	1	A:50-149 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	RELA_STREQ	50-149	1	- B:50-149

(no "Exon" information available for 1VJ7)

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:326
 aligned with RELA_STREQ | Q54089 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:367
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       
           RELA_STREQ     5 INLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVAAHWAYKKGVRGKVNQAEQKVGMNWIKELVEL 371
               SCOP domains d1vj7a1 A:5-196 Stringent response-like protein RelA N-terminal domain                                                                                                                          d1vj7a2 A:197-371 Stringent response-like protein RelA domain 2                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1vj7A02 A:197-329 Beta Polymerase, domain 2                                                                                          ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh--------------..........hhhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhh..hhhh.eeeeee.hhhhhhhhhhhhhhhh.......ee............eeeeee....eeeeeeeehhhhhhhhhh...---------------------hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------HD  PDB: A:50-149 UniProt: 50-149                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vj7 A   5 INLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLG--------------HRKMLMAMSKDIRVILVKLADRLHNMRTL------KQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVAA---------------------NWIKELVEL 371
                                    14        24        34        44        54        64        74        84        94       104    |    -       124       134       144       | -    |  164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      |  -         -       364       
                                                                                                                                  109            124                         152    159                                                                                                                                                                                   341                   363

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with RELA_STREQ | Q54089 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:366
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364      
           RELA_STREQ     5 INLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVAAHWAYKKGVRGKVNQAEQKVGMNWIKELVE 370
               SCOP domains d1vj7b1 B:5-196 Stringent response-like protein RelA N-terminal domain                                                                                                                          d1vj7b2 B:197-      370 Stringent response-like protein R        elA domain 2                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------                   -----------------------------------------------------------------1vj7B02 B:197-      329 Beta Polymerase, domain 2                                                                                    -----------                       ------- CATH domains
           Pfam domains (1) ---------------------------------------------HD-1vj7B01 B:50-149                                                                                 -------------------------------------------------------------      -----------------------RelA_SpoT-1vj7        B03 B:240-340                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------HD-1vj7B02 B:50-149                                                                                 -------------------------------------------------------------      -----------------------RelA_SpoT-1vj7        B04 B:240-340                                                                                         ------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...-------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------hhhhhhhhhhhhhhhh....eeee...hhhhhhhh..--------....eeeeeee.hhhhhhhhhhhhhhhh.......ee............eeeee......eeeeeeehhhhhhhhhh..-----------------------....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------HD  PDB: B:50-149 UniProt: 50-149                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vj7 B   5 INLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVE-------------------SKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEK------LVDDIVTKIKSYTTEQGLFGDVYGRPKHIYSIYRKMR--------IFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVA-----------------------WIKELVE 370
                                    14        24        34        44        54        64        74        84        94       104       | -         -       134       144       154       164       174       184       194       204     |   -  |    224       234       244        |-       264       274       284       294       304       314       324       334     |   -         -       364      
                                                                                                                                     112                 132                                                                           210    217                                 253      262                                                                           340                     364

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta Polymerase; domain 2 (187)

Homologous Superfamily: Beta Polymerase, domain 2 (183)

Equisimilis (Streptococcus dysgalactiae subsp) (1)

1a	1vj7B02	B:197-329
1b	1vj7A02	A:197-329

Asymmetric Unit(hide GO term definitions)

Chain A,B (RELA_STREQ | Q54089)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0008728	GTP diphosphokinase activity	Catalysis of the reaction: ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0008893	guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	Catalysis of the reaction: guanosine 3',5'-bis(diphosphate) + H2O = guanosine 5'-diphosphate + diphosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0015970	guanosine tetraphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
	GO:0015969	guanosine tetraphosphate metabolic process	The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GPX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vj7)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1vj7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RELA_STREQ \| Q54089
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.6.5
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.1.7.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RELA_STREQ \| Q54089
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1VJ7)

(no "Related Entries Specified in the PDB File" available for 1VJ7)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (14, 14)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File