2ZBT - JenaLib

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Title :   CRYSTAL STRUCTURE OF PYRIDOXINE BIOSYNTHESIS PROTEIN FROM THERMUS THERMOPHILUS HB8

Authors :   M. Manzoku, A. Ebihara, Y. Fujimoto, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   29 Oct 07 (Deposition) - 18 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (3x)

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

Reference :   M. Manzoku, A. Ebihara, Y. Fujimoto, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Pyridoxine Biosynthesis Protein From Thermus Thermophilus Hb8
To Be Published
PubMed: search

Molecule 1 - PYRIDOXAL BIOSYNTHESIS LYASE PDXS
	Chains	:	A, B, C, D
	EC Number	:	4.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXS
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MPD	12	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:27 , LYS C:84 , ASP C:105 , GLY C:216 , PHE C:236 , VAL C:237 , GLY C:238	BINDING SITE FOR RESIDUE MPD C 901
2	AC2	SOFTWARE	ASP D:27 , LYS D:84 , ASP D:105 , GLY D:216 , PHE D:236 , VAL D:237 , GLY D:238	BINDING SITE FOR RESIDUE MPD D 902
3	AC3	SOFTWARE	ASP A:27 , LYS A:84 , ASP A:105 , GLY A:216 , PHE A:236 , VAL A:237 , GLY A:238	BINDING SITE FOR RESIDUE MPD A 903
4	AC4	SOFTWARE	ASP B:27 , LYS B:84 , ASP B:105 , GLY B:216 , PHE B:236 , VAL B:237 , GLY B:238	BINDING SITE FOR RESIDUE MPD B 904

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_2	PS51129	PdxS/SNZ family profile.	PDXS_THET8	8-293	4	A:12-278 B:12-278 C:12-278 D:12-278
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDXS_THET8	204-222	4	A:208-226 B:208-226 C:208-226 D:208-226

Biological Unit 1 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_2	PS51129	PdxS/SNZ family profile.	PDXS_THET8	8-293	12	A:12-278 B:12-278 C:12-278 D:12-278
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDXS_THET8	204-222	12	A:208-226 B:208-226 C:208-226 D:208-226

(no "Exon" information available for 2ZBT)

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:276
 aligned with PDXS_THET8 | Q5SKD9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:276
                              1                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           PDXS_THET8     - --MEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 274
               SCOP domains d2zbta_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhh.eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhh.......hhhhhhhhhh.....eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------PDXS_SNZ_2  PDB: A:12-278 UniProt: 8-293                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zbt A   3 GGMEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 278
                                    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

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with PDXS_THET8 | Q5SKD9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
           PDXS_THET8     1 MEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 274
               SCOP domains d2zbtb_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhh.eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhh.......hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PDXS_SNZ_2  PDB: B:12-278 UniProt: 8-293                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbt B   5 MEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 278
                                    14        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:270
 aligned with PDXS_THET8 | Q5SKD9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:270
                                    14        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
           PDXS_THET8     5 TFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 274
               SCOP domains d2zbtc_ C: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....hhhhh.eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhh.......hhhhhhhhhh.....eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee......hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---PDXS_SNZ_2  PDB: C:12-278 UniProt: 8-293                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zbt C   9 TFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 278
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278

Chain D from PDB  Type:PROTEIN  Length:274
 aligned with PDXS_THET8 | Q5SKD9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
           PDXS_THET8     1 MEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 274
               SCOP domains d2zbtd_ D: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........hhhhh..eeeee.hhhhhhhhhhhh..eeee...hhhhhhhh.......hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh...eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee......hhhhhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PDXS_SNZ_2  PDB: D:12-278 UniProt: 8-293                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbt D   5 MEKGTFQIKTGFAEMFKGGVIMDVTTPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGHFVEAMILEAIGVDFIDESEVLTPADEEHHIDKWKFKVPFVCGARNLGEALRRIAEGAAMIRTKGEAGTGNVVEAVRHARTMWKEIRYVQSLREDELMAYAKEIGAPFELVKWVHDHGRLPVVNFAAGGIATPADAALMMHLGMDGVFVGSGIFKSGDPRKRARAIVRAVAHYNDPEVLAEVSEDLGEPM 278
                                    14        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: PdxS-like (6)

Protein domain: automated matches (5)

Thermus thermophilus HB8 [TaxId: 300852] (1)

1a	d2zbta_	A:
1b	d2zbtb_	B:
1c	d2zbtc_	C:
1d	d2zbtd_	D:

(no "CATH Domain" information available for 2ZBT)

(no "Pfam Domain" information available for 2ZBT)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDXS_THET8 | Q5SKD9)

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: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: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: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.

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