3O05 - 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 YEAST PYRIDOXAL 5-PHOSPHATE SYNTHASE SNZ1 COMPLXED WITH SUBSTRATE PLP

Authors :   Y. B. Teng, X. Zhang, Y. X. He, H. X. Hu, C. Z. Zhou

Date :   19 Jul 10 (Deposition) - 24 Nov 10 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Beta Slash Alpha Barrel, (Beat/Alpha)8-Barrel, Pyridoxal 5-Phosphate Synthase, Plp G3P Rbp Sno1, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhang, Y. B. Teng, J. P. Liu, Y. X. He, K. Zhou, Y. Chen, C. Z. Zhou
Structural Insights Into The Catalytic Mechanism Of The Yeast Pyridoxal 5-Phosphate Synthase Snz1
Biochem. J. V. 432 445 2010
PubMed-ID: 20919991 | Reference-DOI: 10.1042/BJ20101241

Molecule 1 - PYRIDOXINE BIOSYNTHESIS PROTEIN SNZ1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 15-297
	Gene	:	SNZ1
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PDX1 HOMOLOG 1, P35

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	PLP	3	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	PLP	6	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:104 , TRP A:111 , HIS A:114 , ARG A:136 , ARG A:137 , LYS A:148 , ARG A:190 , HOH A:335 , HOH A:384 , HOH A:404	BINDING SITE FOR RESIDUE PLP A 1
2	AC2	SOFTWARE	ILE B:83 , GLU B:104 , TRP B:111 , HIS B:114 , LYS B:129 , GLU B:133 , ARG B:136 , ARG B:137 , LYS B:148 , HOH B:309 , HOH B:354 , HOH B:371 , HOH B:373 , HOH B:379	BINDING SITE FOR RESIDUE PLP B 1
3	AC3	SOFTWARE	GLU C:104 , TRP C:111 , HIS C:114 , LYS C:129 , GLU C:133 , ARG C:136 , ARG C:137 , LYS C:148 , HOH C:351 , HOH C:353 , HOH C:361 , HOH C:391	BINDING SITE FOR RESIDUE PLP C 1

(no "SS Bond" information available for 3O05)

(no "Cis Peptide Bond" information available for 3O05)

(no "SAP(SNP)/Variant" information available for 3O05)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	SNZ1_YEAST	205-223	3	A:205-223 B:205-223 C:205-223

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	SNZ1_YEAST	205-223	6	A:205-223 B:205-223 C:205-223

(no "Exon" information available for 3O05)

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:261
 aligned with SNZ1_YEAST | Q03148 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:261
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           SNZ1_YEAST    15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
               SCOP domains d3o05a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhh..eeee...hhhhhhh........hhhhhhhhhh.....eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o05 A  15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with SNZ1_YEAST | Q03148 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:261
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           SNZ1_YEAST    15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
               SCOP domains d3o05b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhh..eeee...hhhhhhh........hhhhhhhhhh.....eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o05 B  15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274

Chain C from PDB  Type:PROTEIN  Length:261
 aligned with SNZ1_YEAST | Q03148 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:261
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           SNZ1_YEAST    15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
               SCOP domains d3o05c_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SOR_SNZ-3o05C01 C:15-212                                                                                                                                                                              --------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) SOR_SNZ-3o05C02 C:15-212                                                                                                                                                                              --------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) SOR_SNZ-3o05C03 C:15-212                                                                                                                                                                              --------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .....eeeee.hhhhhhhhhhhh..eeee...hhhhhhh........hhhhhhhhhh.....eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o05 C  15 MLKGGVIMDVVTPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGHFVEAQIIEALEVDYIDESEVLTPADWTHHIEKDKFKVPFVCGAKDLGEALRRINEGAAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLEKGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSKLLEVSSDLGELM 275
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274

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: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: automated matches (38)

Protein domain: automated matches (38)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (4)

1a	d3o05a_	A:
1b	d3o05b_	B:
1c	d3o05c_	C:

(no "CATH Domain" information available for 3O05)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: SOR_SNZ (6)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

1a	SOR_SNZ-3o05C01	C:15-212
1b	SOR_SNZ-3o05C02	C:15-212
1c	SOR_SNZ-3o05C03	C:15-212

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SNZ1_YEAST | Q03148)

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:0004359	glutaminase activity	Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH3.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0036381	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity	Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH3, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
	GO:0009228	thiamine biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0042819	vitamin B6 biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
cellular component
	GO:1903600	glutaminase complex	A protein complex which is capable of glutaminase activity.

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

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o05)

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
	3o05
		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
	SNZ1_YEAST \| Q03148
		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)
	(no 'Enzyme Classificator' available)
		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
	SNZ1_YEAST \| Q03148
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SNZ1_YEAST \| Q03148	:	3fem 3o06 3o07

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

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 (0, 0)

Pfam Domains (1, 3)

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