3HID - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM YERSINIA PESTIS CO92

Authors :   R. Zhang, M. Zhou, S. Peterson, W. Anderson, A. Joachimiak

Date :   19 May 09 (Deposition) - 02 Jun 09 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Niaid Structural Genomics, Adenylosuccinate Synthetase, Virulence Associated Factor, Pura, Purine Ribonucleotide Biosynthesis, Cytoplasm, Gtp-Binding, Ligase, Magnesium, Metal-Binding, Nucleotide-Binding, Purine Biosynthesis, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, M. Zhou, S. Peterson, W. Anderson, A. Joachimiak
The Crystal Structure Of The Adenylosuccinate Synthetase From Yersinia Pestis Co92
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ADENYLOSUCCINATE SYNTHETASE
	Chains	:	A
	EC Number	:	6.3.4.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19C
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	YERSINIA PESTIS CO92
	Organism Taxid	:	214092
	Strain	:	CO92 / BIOVAR ORIENTALIS
	Synonym	:	IMP--ASPARTATE LIGASE, ADSS, AMPSASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PG6	1	Ligand/Ion	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PG6	2	Ligand/Ion	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:176 , TYR A:177	BINDING SITE FOR RESIDUE PG6 A 433

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

Asymmetric Unit

No.	Residues
1	Tyr A:236	-	Pro A:237

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLOSUCCIN_SYN_1	PS01266	Adenylosuccinate synthetase GTP-binding site.	PURA_YERPE	11-18	1	A:11-18
2	ADENYLOSUCCIN_SYN_2	PS00513	Adenylosuccinate synthetase active site.	PURA_YERPE	133-144	1	A:133-144

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLOSUCCIN_SYN_1	PS01266	Adenylosuccinate synthetase GTP-binding site.	PURA_YERPE	11-18	2	A:11-18
2	ADENYLOSUCCIN_SYN_2	PS00513	Adenylosuccinate synthetase active site.	PURA_YERPE	133-144	2	A:133-144

(no "Exon" information available for 3HID)

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:424
 aligned with PURA_YERPE | Q8ZIV7 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430  
           PURA_YERPE     1 MGKNVVVLGTQWGDEGKGKVVDLLTERAKYVVRYQGGHNAGHTLVINGEKTVLHLIPSGILRENVISIIGNGVVLAPDALMKEMTELEARGVPVRERLLLSEACPLILPYHVALDNAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVSDLFNKETFAIKLKEIVEYHNFQLVHYYKEAAVDYQKVLDDVLAIADILTAMVVDVSELLDNARKQGELIMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGIVKAYSTRVGAGPFPTELNDETGEFLRKQGNEYGATTGRSRRTGWLDIVAVRRAVQINSLSGFCMTKLDVLDGLKEVKLCVGYRMPDGREVDTTPLAAEGWEGIEPIYETMPGWSETTFGVKEHSKLPQAALNYIQRVEELTGVPIDIISTGPDRDETMILRDPFDA 432
               SCOP domains d3hida_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhhh...eeee........eeeee..eeeee............eeee......hhhhhhhhhhhhhhh..hhhhheee.......hhhhhhhhhhhhhh.--------..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeee...hhhhh..............hhhhhhhhhh.hhhhh.eeeeeee.eeee...........hhhhhhhhhhh...........eeeeeehhhhhhhhhhhh..eeeeehhhhhh...eeeeeeeee.....ee.............eeeeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------ADENYLOS------------------------------------------------------------------------------------------------------------------ADENYLOSUCCI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hid A   1 MGKNVVVLGTQWGDEGKGKVVDLLTERAKYVVRYQGGHNAGHTLVINGEKTVLHLIPSGILRENVISIIGNGVVLAPDALMKEMTELEARGVPVRERLLLSEACPLILPYHVALDNAREKAR--------GRGIGPAYEDKVARRGLRVSDLFNKETFAIKLKEIVEYHNFQLVHYYKEAAVDYQKVLDDVLAIADILTAMVVDVSELLDNARKQGELIMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGIVKAYSTRVGAGPFPTELNDETGEFLRKQGNEYGATTGRSRRTGWLDIVAVRRAVQINSLSGFCMTKLDVLDGLKEVKLCVGYRMPDGREVDTTPLAAEGWEGIEPIYETMPGWSETTFGVKEHSKLPQAALNYIQRVEELTGVPIDIISTGPDRDETMILRDPFDA 432
                                    10        20        30        40        50        60        70        80        90       100       110       120 |       -|      140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430  
                                                                                                                                                   122      131

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: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nitrogenase iron protein-like (152)

Protein domain: automated matches (19)

Yersinia pestis [TaxId: 214092] (1)

d3hida_

(no "CATH Domain" information available for 3HID)

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

Asymmetric Unit(hide GO term definitions)

Chain A (PURA_YERPE | Q8ZIV7)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0004019	adenylosuccinate synthase activity	Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H(+) + phosphate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
biological process
	GO:0044208	'de novo' AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
	GO:0046040	IMP metabolic process	The chemical reactions and pathways involving IMP, inosine monophosphate.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		PG6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:236 - Pro A:237	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	3hid
		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
	PURA_YERPE \| Q8ZIV7
		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)
	6.3.4.4
		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
	PURA_YERPE \| Q8ZIV7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3HID)

(no "Related Entries Specified in the PDB File" available for 3HID)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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