4ADU - JenaLib

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Title :   CRYSTAL STRUCTURE OF PLASMODIAL PLP SYNTHASE WITH BOUND R5P INTERMEDIATE

Authors :   G. Guedez, I. Sinning, I. Tews

Date :   03 Jan 12 (Deposition) - 25 Jan 12 (Release) - 25 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.44

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)

Keywords :   Transferase, Synthase, Pyridoxal 5-Phosphate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Guedez, K. Hipp, V. Windeisen, B. Derrer, M. Gengenbacher, B. Boettcher, I. Sinning, B. Kappes, I. Tews
Assembly Of The Eukaryotic Plp-Synthase Complex From Plasmodium And Activation Of The Pdx1 Enzyme.
Structure V. 20 172 2012
PubMed-ID: 22244765 | Reference-DOI: 10.1016/J.STR.2011.11.015

Molecule 1 - PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21-A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIL
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PLASMODIUM BERGHEI
	Organism Taxid	:	5821
	Strain	:	NK65

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	R5P	2	Ligand/Ion	RIBOSE-5-PHOSPHATE

Biological Unit 1 (2, 42)

No.	Name	Count	Type	Full Name
1	EDO	30	Ligand/Ion	1,2-ETHANEDIOL
2	R5P	12	Ligand/Ion	RIBOSE-5-PHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	EDO A:303	BINDING SITE FOR RESIDUE EDO A 302
2	AC2	SOFTWARE	EDO A:302 , EDO A:305	BINDING SITE FOR RESIDUE EDO A 303
3	AC3	SOFTWARE	EDO A:305 , EDO A:306 , HOH A:2087 , TYR B:176	BINDING SITE FOR RESIDUE EDO A 304
4	AC4	SOFTWARE	EDO A:303 , EDO A:304 , EDO A:306	BINDING SITE FOR RESIDUE EDO A 305
5	AC5	SOFTWARE	EDO A:304 , EDO A:305 , TYR B:176	BINDING SITE FOR RESIDUE EDO A 306
6	AC6	SOFTWARE	ASP A:27 , PRO A:52 , LYS A:84 , ASP A:105 , ALA A:155 , GLY A:156 , GLY A:216 , GLY A:217 , PHE A:236 , VAL A:237 , GLY A:238 , SER A:239 , HOH A:2075	BINDING SITE FOR RESIDUE R5P A1084
7	AC7	SOFTWARE	ASP B:27 , PRO B:52 , LYS B:84 , ASP B:105 , SER B:107 , VAL B:109 , ALA B:155 , GLY B:156 , GLY B:216 , GLY B:217 , GLY B:238 , SER B:239 , HOH B:2039 , HOH B:2050 , HOH B:2051	BINDING SITE FOR RESIDUE R5P B1084

(no "SS Bond" information available for 4ADU)

(no "Cis Peptide Bond" information available for 4ADU)

(no "SAP(SNP)/Variant" information available for 4ADU)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_2	PS51129	PdxS/SNZ family profile.	PDX1_PLABE	12-297	2	A:12-284 B:12-283
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDX1_PLABE	208-226	2	A:208-226 B: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.	PDX1_PLABE	12-297	12	A:12-284 B:12-283
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDX1_PLABE	208-226	12	A:208-226 B:208-226

(no "Exon" information available for 4ADU)

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:278
 aligned with PDX1_PLABE | P0DMS0 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
           PDX1_PLABE     7 NDSILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTKV 284
               SCOP domains d4adua_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee...hhhhhh.........hhhhhhhhhh....eeeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----PDXS_SNZ_2  PDB: A:12-284 UniProt: 12-297                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ---------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4adu A   7 NDSILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTKV 284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain A from PDB  Type:PROTEIN  Length:278
 aligned with Q4Z0E8_PLABA | Q4Z0E8 from UniProtKB/TrEMBL  Length:297

    Alignment length:278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
         Q4Z0E8_PLABA     7 NDSILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTKV 284
               SCOP domains d4adua_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee...hhhhhh.........hhhhhhhhhh....eeeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4adu A   7 NDSILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTKV 284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with PDX1_PLABE | P0DMS0 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:274
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
           PDX1_PLABE    10 ILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTK 283
               SCOP domains d4adub_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee..................hhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDXS_SNZ_2  PDB: B:12-283 UniProt: 12-297                                                                                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4adu B  10 ILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTK 283
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with Q4Z0E8_PLABA | Q4Z0E8 from UniProtKB/TrEMBL  Length:297

    Alignment length:274
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
         Q4Z0E8_PLABA    10 ILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTK 283
               SCOP domains d4adub_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee..................hhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4adu B  10 ILLKHGWCEMLKGGVIMDVKNVEQAKIAEKAGAIGVMILENIPSELRNTDGVARSVDPLKIEEIRKCISINVLAKVRIGHFVEAQILEELKVDMLDESEVLTMADEYNHINKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKLKRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVSNFNNPKILLNVSLGLGKAMHGNTK 283
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279

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)

Plasmodium berghei [TaxId: 5821] (2)

1a	d4adua_	A:
1b	d4adub_	B:

(no "CATH Domain" information available for 4ADU)

(no "Pfam Domain" information available for 4ADU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDX1_PLABE | P0DMS0)

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.

Chain A,B (Q4Z0E8_PLABA | Q4Z0E8)

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.
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.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 4adu)

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4ads	CRYSTAL STRUCTURE OF PLASMODIAL PLP SYNTHASE COMPLEX
4adt	CRYSTAL STRUCTURE OF PLASMODIAL PLP SYNTHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (6, 10)

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Related Entries

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Related Entries Specified in the PDB File