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Title :   PDXA PROTEIN; NAD-DEPENDENT DEHYDROGENASE/CARBOXYLASE; SUBUNIT OF PYRIDOXINE PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ-PDXA [SALMONELLA TYPHIMURIUM]

Authors :   J. Osipiuk, P. Quartey, S. Moy, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   27 Oct 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Nad-Dependent Dehydrogenase/Carboxylase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, P. Quartey, S. Moy, F. Collart, A. Joachimiak
Crystal Structure Of Nad-Dependent Dehydrogenase/Carboxylase Of Salmonella Typhimurium
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE 1
	Chains	:	A, B
	EC Number	:	1.1.1.262
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXA, STM0090
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	4-(PHOSPHOHYDROXY)-L-THREONINE DEHYDROGENASE 1, NAD-DEPENDENT DEHYDROGENASE/CARBOXYLASE, PYRIDOXINE PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ-PDXA SUBUNIT, PDXA PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 20)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CO	2	Ligand/Ion	COBALT (II) ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:211 , HOH A:1003 , HIS B:166 , HIS B:266 , HOH B:999 , HOH B:1008	BINDING SITE FOR RESIDUE CO B 901
2	AC2	SOFTWARE	HIS A:166 , HIS A:266 , HOH A:995 , HOH A:1015 , HIS B:211 , HOH B:1006	BINDING SITE FOR RESIDUE CO A 902
3	AC3	SOFTWARE	ARG A:143	BINDING SITE FOR RESIDUE CL A 903
4	AC4	SOFTWARE	HIS A:136 , THR A:137 , MSE A:151 , HIS A:166 , ASN A:283 , ARG A:292 , HOH A:994 , HOH A:1076	BINDING SITE FOR RESIDUE SO4 A 990
5	AC5	SOFTWARE	GLY B:135 , HIS B:136 , THR B:137 , MSE B:151 , HIS B:166 , ASN B:283 , ARG B:292 , HOH B:997 , HOH B:1071	BINDING SITE FOR RESIDUE SO4 B 991
6	AC6	SOFTWARE	HIS A:189 , HIS A:190 , ARG A:193 , HOH A:1144 , HOH B:1064	BINDING SITE FOR RESIDUE SO4 A 992

(no "SS Bond" information available for 1R8K)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:242	-	Pro A:243
2	Gly B:242	-	Pro B:243

(no "SAP(SNP)/Variant" information available for 1R8K)

(no "PROSITE Motif" information available for 1R8K)

(no "Exon" information available for 1R8K)

Asymmetric/Biological 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:327
 aligned with PDXA_SALTY | P58717 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:327
                                    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       322       
           PDXA_SALTY     3 SAQRVVITPGEPAGSGPDLVVQLAQRAWPIELVVCADGALLTERAAMLGLPLSLLPYSPDVPAAPQPAGTLTLLPVSLRAPAISGQLTVENGPYVVETLARACDGCLNGEFAALITGPVHKGVINDAGISFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRAIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLDELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ 329
               SCOP domains d1r8ka_ A: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1r8kA00 A:3-329 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhh......eeeeeehhhhhhhhhhhh....eeee.............eeeeee............hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhh......hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh...eeeee.....eee................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8k A   3 SAQRVVITPGEPAGSGPDLVVQLAQRAWPIELVVCADGALLTERAAmLGLPLSLLPYSPDVPAAPQPAGTLTLLPVSLRAPAISGQLTVENGPYVVETLARACDGCLNGEFAALITGPVHKGVINDAGISFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRAIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLDELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNTQ 329
                                    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       322 |     
                                                                         49-MSE                                                                                               151-MSE                                                            218-MSE             238-MSE                   264-MSE                                                     324-MSE 
                                                                                                                                                                               152-MSE

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with PDXA_SALTY | P58717 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:326
                                    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       322      
           PDXA_SALTY     3 SAQRVVITPGEPAGSGPDLVVQLAQRAWPIELVVCADGALLTERAAMLGLPLSLLPYSPDVPAAPQPAGTLTLLPVSLRAPAISGQLTVENGPYVVETLARACDGCLNGEFAALITGPVHKGVINDAGISFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRAIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLDELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNT 328
               SCOP domains d1r8kb_ B: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1r8kB00 B:3-328 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhh......eeee..hhhhhhhhhhhh....eeee.............eeee.................hhhhhhhhhhhhhhhhhh....eeee...hhhhhhh......hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhh.....eeeee....eeee.....hhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8k B   3 SAQRVVITPGEPAGSGPDLVVQLAQRAWPIELVVCADGALLTERAAmLGLPLSLLPYSPDVPAAPQPAGTLTLLPVSLRAPAISGQLTVENGPYVVETLARACDGCLNGEFAALITGPVHKGVINDAGISFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRAIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLDELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNT 328
                                    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       322 |    
                                                                         49-MSE                                                                                               151-MSE                                                            218-MSE             238-MSE                   264-MSE                                                     324-MSE
                                                                                                                                                                               152-MSE

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: PdxA-like (6)

Protein domain: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA (4)

Salmonella typhimurium [TaxId: 90371] (1)

1a	d1r8ka_	A:
1b	d1r8kb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Salmonella typhimurium. Organism_taxid: 602. (2)

1a	1r8kA00	A:3-329
1b	1r8kB00	B:3-328

(no "Pfam Domain" information available for 1R8K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXA_SALTY | P58717)

molecular function
	GO:0050570	4-hydroxythreonine-4-phosphate dehydrogenase activity	Catalysis of the reaction: 4-(phosphonooxy)-threonine + NAD+ = 2-amino-3-oxo-4-phosphonooxybutyrate + NADH + H+.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:242 - Pro A:243	[ RasMol ]
		Gly B:242 - Pro B:243	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 20)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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