1G2Q - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE

Authors :   W. Shi, K. S. E. Tanaka, S. C. Almo, V. L. Schramm

Date :   20 Oct 00 (Deposition) - 05 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dimer, Single Domain, Catalytic Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Shi, K. S. Tanaka, T. R. Crother, M. W. Taylor, S. C. Almo, V. L. Schramm
Structural Analysis Of Adenine Phosphoribosyltransferase From Saccharomyces Cerevisiae.
Biochemistry V. 40 10800 2001
PubMed-ID: 11535055 | Reference-DOI: 10.1021/BI010465H
(for further references see the PDB file header)

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE 1
	Chains	:	A, B
	EC Number	:	2.4.2.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1G2Q)

(no "Site" information available for 1G2Q)

(no "SS Bond" information available for 1G2Q)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:20	-	Pro A:21
2	Glu A:67	-	Ser A:68
3	Phe B:20	-	Pro B:21
4	Glu B:67	-	Ser B:68

(no "SAP(SNP)/Variant" information available for 1G2Q)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUR_PYR_PR_TRANSFER	PS00103	Purine/pyrimidine phosphoribosyl transferases signature.	APT1_YEAST	125-137	2	A:125-137 B:125-137

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML022W	1	YML022W.1	XIII:228937-229500	564	APT1_YEAST	1-187	187	2	A:1-178 B:1-178	178 178

Asymmetric/Biological 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:178
 aligned with APT1_YEAST | P49435 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           APT1_YEAST     1 MSIASYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
               SCOP domains d1g2qa_ A: Adenine PRTase                                                                                                                                                          SCOP domains
               CATH domains 1g2qA00 A:1-178  [code=3.40.50.2020, no name defined]                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR----------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-178 UniProt: 1-187 [INCOMPLETE]                                                                                                                                 Transcript 1
                 1g2q A   1 MPIASYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with APT1_YEAST | P49435 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           APT1_YEAST     1 MSIASYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
               SCOP domains d1g2qb_ B: Adenine PRTase                                                                                                                                                          SCOP domains
               CATH domains 1g2qB00 B:1-178  [code=3.40.50.2020, no name defined]                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR----------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-178 UniProt: 1-187 [INCOMPLETE]                                                                                                                                 Transcript 1
                 1g2q B   1 MPIASYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: Phosphoribosyltransferases (PRTases) (100)

Protein domain: Adenine PRTase (13)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1g2qa_	A:
1b	d1g2qb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2020, no name defined] (117)

Baker's yeast (Saccharomyces cerevisiae) (5)

1a	1g2qA00	A:1-178
1b	1g2qB00	B:1-178

(no "Pfam Domain" information available for 1G2Q)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (APT1_YEAST | P49435)

molecular function
	GO:0003999	adenine phosphoribosyltransferase activity	Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006167	AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
	GO:0044209	AMP salvage	The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
	GO:0006168	adenine salvage	Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0006166	purine ribonucleoside salvage	Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 1g2q)

	Sites
(no "Sites" information available for 1g2q)

	Cis Peptide Bonds
		Glu A:67 - Ser A:68	[ RasMol ]
		Glu B:67 - Ser B:68	[ RasMol ]
		Phe A:20 - Pro A:21	[ RasMol ]
		Phe B:20 - Pro B:21	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	1g2q
		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
	APT1_YEAST \| P49435
		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)
	2.4.2.7
		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
	APT1_YEAST \| P49435
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	APT1_YEAST \| P49435	:	1g2p

1g2p	1G2P CONTAINS THE SAME PROTEIN WITH TWO SULFATE IONS IN THE ACRIVE SITE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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