1A69 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE)

Authors :   G. Koellner, M. Luic, D. Shugar, W. Saenger, A. Bzowska

Date :   08 Mar 98 (Deposition) - 14 Oct 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Glycosyltransferase, Purine Nucleoside Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Koellner, M. Luic, D. Shugar, W. Saenger, A. Bzowska
Crystal Structure Of The Ternary Complex Of E. Coli Purine Nucleoside Phosphorylase With Formycin B, A Structural Analogue Of The Substrate Inosine, And Phosphate (Sulphate) At 2. 1 A Resolution.
J. Mol. Biol. V. 280 153 1998
PubMed-ID: 9653038 | Reference-DOI: 10.1006/JMBI.1998.1799

Molecule 1 - PURINE NUCLEOSIDE PHOSPHORYLASE
	Chains	:	A, B, C
	EC Number	:	2.4.2.1
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	FMB	3	Ligand/Ion	FORMYCIN B
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	FMB	6	Ligand/Ion	FORMYCIN B
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:19 , GLY A:20 , ARG A:24 , ARG A:87 , GLY A:89 , SER A:90 , FMB A:240 , ARG C:43	BINDING SITE FOR RESIDUE SO4 A 239
2	AC2	SOFTWARE	ARG A:87 , SER A:90 , CYS A:91 , GLY A:92 , PHE A:159 , VAL A:178 , GLU A:179 , MET A:180 , GLU A:181 , SER A:203 , ASP A:204 , SO4 A:239 , HOH A:264 , HOH A:265 , HOH A:268 , HIS C:4	BINDING SITE FOR RESIDUE FMB A 240
3	AC3	SOFTWARE	GLY B:20 , ARG B:24 , ARG B:43 , ARG B:87 , SER B:90 , FMB B:240	BINDING SITE FOR RESIDUE SO4 B 239
4	AC4	SOFTWARE	HIS B:4 , MET B:64 , ARG B:87 , SER B:90 , GLY B:92 , PHE B:159 , VAL B:178 , GLU B:179 , MET B:180 , GLU B:181 , ASP B:204 , SO4 B:239 , HOH B:364	BINDING SITE FOR RESIDUE FMB B 240
5	AC5	SOFTWARE	ARG A:43 , GLY C:20 , ARG C:87 , GLY C:89 , SER C:90 , FMB C:240 , HOH C:265	BINDING SITE FOR RESIDUE SO4 C 239
6	AC6	SOFTWARE	HIS A:4 , ARG C:87 , SER C:90 , CYS C:91 , GLY C:92 , PHE C:159 , VAL C:178 , GLU C:179 , MET C:180 , GLU C:181 , SER C:203 , ASP C:204 , SO4 C:239 , HOH C:268	BINDING SITE FOR RESIDUE FMB C 240
7	AVE	UNKNOWN	ARG A:24 , SER A:90 , ARG A:217 , ASP A:204 , GLY A:20 , ARG A:87 , ARG A:43 , GLU A:181 , MET A:180 , HIS A:4	BINDING SITE OF FORMYCIN B AND PHOSPHATE.

(no "SS Bond" information available for 1A69)

(no "Cis Peptide Bond" information available for 1A69)

(no "SAP(SNP)/Variant" information available for 1A69)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	DEOD_ECOLI	62-77	3	A:61-76 B:61-76 C:61-76

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	DEOD_ECOLI	62-77	6	A:61-76 B:61-76 C:61-76

(no "Exon" information available for 1A69)

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 DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1a69a_ A: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1a69A00 A:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...hhhhhhhhhh.....eeee.hhh..eeeeee..eeeeee.....hhhhhhhhhhhhhh....eeeeeeeeee.........eeeeeeeee...hhhhh...........hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhh....eee..hhhhhhhhhh...eeeeeeeeeee........hhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a69 A   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 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 DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1a69b_ B: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1a69B00 B:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...hhhhhhhhhh.....eeee.hhh..eeeeee..eeeeee.....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee...hhhhh...........hhhhhhhhhhhhhh....eeeeeee........hhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a69 B   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 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 C from PDB  Type:PROTEIN  Length:233
 aligned with DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1a69c_ C: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1a69C00 C:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...hhhhhhhhhhh....eeee.hhh..eeeeee..eeeeee.....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee...hhhhh...........hhhhhhhhhhhhhh....eeeeeee........hhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeeeee..----..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a69 C   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIR----TTAAERQTTFNDMIKIALESVLLGDK 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  - |     220       230       
                                                                                                                                                                                                                                        207  212

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: Phosphorylase/hydrolase-like (558)

Superfamily: Purine and uridine phosphorylases (283)

Family: Purine and uridine phosphorylases (224)

Protein domain: Purine nucleoside phosphorylase, PNP (93)

Escherichia coli [TaxId: 562] (24)

1a	d1a69a_	A:
1b	d1a69b_	B:
1c	d1a69c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1580, no name defined] (194)

Escherichia coli. Organism_taxid: 562 (2)

1a	1a69A00	A:1-237
1b	1a69B00	B:1-237
1c	1a69C00	C:1-237

(no "Pfam Domain" information available for 1A69)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DEOD_ECOLI | P0ABP8)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0004731	purine-nucleoside phosphorylase activity	Catalysis of the reaction: purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
	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).
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	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:0006152	purine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0019686	purine nucleoside interconversion	The chemical reactions and pathways by which a purine nucleoside is synthesized from another purine nucleoside.
	GO:0042278	purine nucleoside metabolic process	The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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
		FMB	[ 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 ]
		AVE	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1a69)

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
	1a69
		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
	DEOD_ECOLI \| P0ABP8
		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)
	2.4.2.1
		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
	DEOD_ECOLI \| P0ABP8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1A69)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

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