1YPF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GUAC (BA5705) FROM BACILLUS ANTHRACIS AT 1.8 A RESOLUTION

Authors :   R. Grenha, V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, A. J. Wilkinson, K. S. Wilson, Structural Proteomics In Europe (S

Date :   31 Jan 05 (Deposition) - 14 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Guac, Purines, Pyrimidines, Nucleosides, Nucleotides, Nucleotide And Nucleoside Interconversions, Spine, Structural Genomics, Structural Proteomics In Europe, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Grenha, V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, A. J. Wilkinson, K. S. Wilson
Crystal Structure Of Guac (Ba5705) From Bacillus Anthracis At 1. 8 A Resolution
To Be Published
PubMed: search

Molecule 1 - GMP REDUCTASE
	Chains	:	A, B
	EC Number	:	1.7.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-YSBLIC
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GUAC
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392
	Synonym	:	GUANOSINE MONOPHOSPHATE REDUCTASE, GUANOSINE 5'- MONOPHOSPHATE OXIDOREDUCTASE

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1YPF)

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

Asymmetric Unit

No.	Residues
1	Gly A:146	-	Asn A:147
2	Gly B:146	-	Asn B:147

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_DH_GMP_RED	PS00487	IMP dehydrogenase / GMP reductase signature.	GUAC_BACAN	165-177	2	A:165-177 B:165-177

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_DH_GMP_RED	PS00487	IMP dehydrogenase / GMP reductase signature.	GUAC_BACAN	165-177	4	A:165-177 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_DH_GMP_RED	PS00487	IMP dehydrogenase / GMP reductase signature.	GUAC_BACAN	165-177	1	- B:165-177

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_DH_GMP_RED	PS00487	IMP dehydrogenase / GMP reductase signature.	GUAC_BACAN	165-177	4	- B:165-177

(no "Exon" information available for 1YPF)

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:295
 aligned with GUAC_BACAN | Q81JJ9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:318
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        
           GUAC_BACAN     3 NVFDYEDIQLIPAKCIVNSRSECDTTVTLGKHKFKLPVVPANMQTIIDERIATYLAENNYFYIMHRFQPEKRISFIRDMQSRGLIASISVGVKEDEYEFVQQLAAEHLTPEYITIDIAHGHSNAVINMIQHIKKHLPESFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKIKTGFGTGGWQLAALRWCAKAASKPIIADGGIRTNGDVAKSIRFGATMVMIGSLFAGHEESPGETIEKDGKLYKEYFGSASEFQKGEKKNVEGKKMFVEHKGSLEDTLIEMEQDLQSSISYAGGTKLDSIRTVDYVVVKNSI 320
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ypfA00 A:3-320 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eee........hhhhh...eee..eee...eee.......hhhhhhhhhhh.........hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee.......hhhhhhhh.....hhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeeehhhhh..........-----------------------.............hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------IMP_DH_GMP_RE----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ypf A   3 NVFDYEDIQLIPAKCIVNSRSECDTTVTLGKHKFKLPVVPANMQTIIDERIATYLAENNYFYIMHRFQPEKRISFIRDMQSRGLIASISVGVKEDEYEFVQQLAAEHLTPEYITIDIAHGHSNAVINMIQHIKKHLPESFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKIKTGFGTGGWQLAALRWCAKAASKPIIADGGIRTNGDVAKSIRFGATMVMIGSLFAGHEESPGETI-----------------------NVEGKKMFVEHKGSLEDTLIEMEQDLQSSISYAGGTKLDSIRTVDYVVVKNSI 320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 |       -         -     | 272       282       292       302       312        
                                                                                                                                                                                                                                                                           244                     268

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with GUAC_BACAN | Q81JJ9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
           GUAC_BACAN     2 GNVFDYEDIQLIPAKCIVNSRSECDTTVTLGKHKFKLPVVPANMQTIIDERIATYLAENNYFYIMHRFQPEKRISFIRDMQSRGLIASISVGVKEDEYEFVQQLAAEHLTPEYITIDIAHGHSNAVINMIQHIKKHLPESFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKIKTGFGTGGWQLAALRWCAKAASKPIIADGGIRTNGDVAKSIRFGATMVMIGSLFAGHEESPGETIEKDGKLYKEYFGSASEFQKGEKKNVEGKKMFVEHKGSLEDTLIEMEQDLQSSISYAGGTKLDSIRTVDYVVVKNS 319
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ypfB00 B:2-319 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) -IMPDH-1ypfB01 B:3-319                                                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) -IMPDH-1ypfB02 B:3-319                                                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ....hhh.eee........hhhhh...eee..eee...eee.......hhhhhhhhhhh.........hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee.......hhhhhhhh.....hhhhhhhhhhh.....eeee.....hhhhhhhhhh...eeeehhhhh............-----------------------...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------IMP_DH_GMP_RE---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ypf B   2 GNVFDYEDIQLIPAKCIVNSRSECDTTVTLGKHKFKLPVVPANMQTIIDERIATYLAENNYFYIMHRFQPEKRISFIRDMQSRGLIASISVGVKEDEYEFVQQLAAEHLTPEYITIDIAHGHSNAVINMIQHIKKHLPESFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKIKTGFGTGGWQLAALRWCAKAASKPIIADGGIRTNGDVAKSIRFGATMVMIGSLFAGHEESPGETIEK-----------------------EGKKMFVEHKGSLEDTLIEMEQDLQSSISYAGGTKLDSIRTVDYVVVKNS 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    |    -         -       271       281       291       301       311        
                                                                                                                                                                                                                                                                              246                     270

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 '\|'

(no "SCOP Domain" information available for 1YPF)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Bacillus anthracis. Organism_taxid: 1392. (4)

1a	1ypfA00	A:3-320
1b	1ypfB00	B:2-319

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: IMPDH (16)

Bacillus anthracis (1)

1a	IMPDH-1ypfB01	B:3-319
1b	IMPDH-1ypfB02	B:3-319

Asymmetric Unit(hide GO term definitions)

Chain A,B (GUAC_BACAN | Q81JJ9)

molecular function
	GO:0003920	GMP reductase activity	Catalysis of the reaction: IMP + NADP(+) + NH(4)(+) = GMP + 2 H(+) + NADPH.
	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:0004152	dihydroorotate dehydrogenase activity	Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving 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:1902560	GMP reductase complex	An oxidoreductase complex which is capable of GMP reductase activity. It catalyses the irreversible reaction: GMP + 2 H(+) + NADPH => IMP + NADP(+) + NH(4)(+).

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
(no "Ligands, Modified Residues, Ions" information available for 1ypf)

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

	Cis Peptide Bonds
		Gly A:146 - Asn A:147	[ RasMol ]
		Gly B:146 - Asn B:147	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	1ypf
		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
	GUAC_BACAN \| Q81JJ9
		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)
	1.7.1.7
		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
	GUAC_BACAN \| Q81JJ9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GUAC_BACAN \| Q81JJ9	:	2a1y

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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