2YWV - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SAICAR SYNTHETASE FROM GEOBACILLUS KAUSTOPHILUS

Authors :   M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)

Date :   23 Apr 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)

Keywords :   Adp Complex, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Saicar Synthetase From Geobacillus Kaustophilus
To Be Published
PubMed: search

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE SUCCINOCARBOXAMIDE SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.3.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-HISTEV
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS
	Organism Taxid	:	1462

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG B:95 , GLY B:100 , SER B:101 , ARG B:201 , HOH B:823 , HOH B:901 , HOH B:914	BINDING SITE FOR RESIDUE SO4 B 541
02	AC2	SOFTWARE	ALA B:35 , PHE B:36 , ASN B:37 , LYS B:213 , ARG B:217 , HOH B:881 , HOH B:912	BINDING SITE FOR RESIDUE SO4 B 542
03	AC3	SOFTWARE	ARG A:95 , GLY A:100 , SER A:101 , ARG A:201 , HOH A:807 , HOH A:821 , HOH A:904	BINDING SITE FOR RESIDUE SO4 A 543
04	AC4	SOFTWARE	ALA A:35 , PHE A:36 , ASN A:37 , LYS A:213 , ARG A:217 , HOH A:858	BINDING SITE FOR RESIDUE SO4 A 544
05	AC5	SOFTWARE	VAL A:97 , ARG A:164 , ARG A:173 , HOH A:793 , HOH A:826 , HOH A:957	BINDING SITE FOR RESIDUE SO4 A 545
06	AC6	SOFTWARE	VAL B:97 , ARG B:173 , HOH B:779 , HOH B:799 , HOH B:820	BINDING SITE FOR RESIDUE SO4 B 546
07	AC7	SOFTWARE	ARG A:105 , PRO A:131 , LEU A:132 , ARG B:105 , HOH B:782 , HOH B:933	BINDING SITE FOR RESIDUE SO4 B 548
08	AC8	SOFTWARE	ASP A:193 , ADP A:600 , HOH A:706 , HOH A:709 , HOH A:787 , HOH A:798	BINDING SITE FOR RESIDUE MG A 701
09	AC9	SOFTWARE	ADP B:601 , HOH B:708 , HOH B:709 , HOH B:713 , HOH B:812	BINDING SITE FOR RESIDUE MG B 702
10	BC1	SOFTWARE	TYR A:9 , GLY A:11 , LYS A:12 , ALA A:13 , LYS A:14 , ILE A:16 , LEU A:25 , HIS A:70 , ARG A:83 , VAL A:85 , ILE A:87 , LYS A:124 , GLU A:180 , ASP A:193 , MG A:701 , HOH A:706 , HOH A:833 , HOH A:862	BINDING SITE FOR RESIDUE ADP A 600
11	BC2	SOFTWARE	TYR B:9 , GLY B:11 , LYS B:12 , ALA B:13 , LYS B:14 , ILE B:16 , LEU B:25 , HIS B:70 , ARG B:83 , VAL B:85 , ILE B:87 , LYS B:124 , GLU B:180 , ASP B:193 , MG B:702 , HOH B:708 , HOH B:735 , HOH B:877	BINDING SITE FOR RESIDUE ADP B 601

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

(no "Cis Peptide Bond" information available for 2YWV)

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

(no "PROSITE Motif" information available for 2YWV)

(no "Exon" information available for 2YWV)

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:237
 aligned with Q5L3D5_GEOKA | Q5L3D5 from UniProtKB/TrEMBL  Length:242

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q5L3D5_GEOKA     1 MPTKQQLLYEGKAKKIYATDEPDVLWVEYKDSATAFNGEKKATIAGKGRLNNEISSLLFLKLREAGIANHFIEKLSPTEQLVRRVTIIPLEVVVRNVVAGSLAKRIGLEEGTPLEAPLVEFYYKNDDLGDPLLLEDHIFILKLASREEVAALKQAALAVNDVLRLHFAERNVRLIDFKLEFGRTADGAILLADEISPDTCRLWDAKTNEKLDKDVFRRDLGSLTDAYEVILQRLGGE 237
               SCOP domains d2ywva_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------2ywvA02 A:86-222 ATP-grasp fold, B domain                                                                                                --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeeeehhhhhhhhh....eeeeeeeeeeee.hhhhh..eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eee.....eee........eeeee........hhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywv A   1 MPTKQQLLYEGKAKKIYATDEPDVLWVEYKDSATAFNGEKKATIAGKGRLNNEISSLLFLKLREAGIANHFIEKLSPTEQLVRRVTIIPLEVVVRNVVAGSLAKRIGLEEGTPLEAPLVEFYYKNDDLGDPLLLEDHIFILKLASREEVAALKQAALAVNDVLRLHFAERNVRLIDFKLEFGRTADGAILLADEISPDTCRLWDAKTNEKLDKDVFRRDLGSLTDAYEVILQRLGGE 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with Q5L3D5_GEOKA | Q5L3D5 from UniProtKB/TrEMBL  Length:242

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q5L3D5_GEOKA     1 MPTKQQLLYEGKAKKIYATDEPDVLWVEYKDSATAFNGEKKATIAGKGRLNNEISSLLFLKLREAGIANHFIEKLSPTEQLVRRVTIIPLEVVVRNVVAGSLAKRIGLEEGTPLEAPLVEFYYKNDDLGDPLLLEDHIFILKLASREEVAALKQAALAVNDVLRLHFAERNVRLIDFKLEFGRTADGAILLADEISPDTCRLWDAKTNEKLDKDVFRRDLGSLTDAYEVILQRLGGE 237
               SCOP domains d2ywvb_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------2ywvB02 B:86-222 ATP-grasp fold, B domain                                                                                                --------------- CATH domains
           Pfam domains (1) ---SAICAR_synt-2ywvB01 B:4-237                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ---SAICAR_synt-2ywvB02 B:4-237                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author ...eeeeeee...eeeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhhhh.....eeeeeeeeeee.hhhhh..eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee.....eeee.......eeeee........hhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywv B   1 MPTKQQLLYEGKAKKIYATDEPDVLWVEYKDSATAFNGEKKATIAGKGRLNNEISSLLFLKLREAGIANHFIEKLSPTEQLVRRVTIIPLEVVVRNVVAGSLAKRIGLEEGTPLEAPLVEFYYKNDDLGDPLLLEDHIFILKLASREEVAALKQAALAVNDVLRLHFAERNVRLIDFKLEFGRTADGAILLADEISPDTCRLWDAKTNEKLDKDVFRRDLGSLTDAYEVILQRLGGE 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: SAICAR synthase-like (28)

Superfamily: SAICAR synthase-like (28)

Family: automated matches (12)

Protein domain: automated matches (12)

Geobacillus kaustophilus [TaxId: 1462] (1)

1a	d2ywva_	A:
1b	d2ywvb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: ATP-grasp fold, B domain (118)

Geobacillus kaustophilus. Organism_taxid: 1462. (5)

1a	2ywvA02	A:86-222
1b	2ywvB02	B:86-222

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SAICAR_synt] (7)

Family: SAICAR_synt (7)

Geobacillus kaustophilus (1)

1a	SAICAR_synt-2ywvB01	B:4-237
1b	SAICAR_synt-2ywvB02	B:4-237

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5L3D5_GEOKA | Q5L3D5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0004639	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity	Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate.
biological process
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	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.

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
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ywv)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	2ywv
		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
	Q5L3D5_GEOKA \| Q5L3D5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	6.3.2.6
		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
	Q5L3D5_GEOKA \| Q5L3D5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2YWV)

(no "Related Entries Specified in the PDB File" available for 2YWV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

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