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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI PDXA
 
Authors :  J. Sivaraman, Y. Li, J. Banks, D. E. Cane, A. Matte, M. Cygler
Date :  20 Jun 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Pyridoxine Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sivaraman, Y. Li, J. Banks, D. E. Cane, A. Matte, M. Cygler
Crystal Structure Of Escherichia Coli Pdxa, An Enzyme Involved In The Pyridoxal Phosphate Biosynthesis Pathway
J. Biol. Chem. V. 278 43682 2003
PubMed-ID: 12896974  |  Reference-DOI: 10.1074/JBC.M306344200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.262
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PF04
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDXA OR B0052
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 4- PHOSPHOHYDROXY, -L-THREONINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 32)

Asymmetric Unit (2, 32)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:211 , HIS B:166 , HIS B:266 , HOH B:440BINDING SITE FOR RESIDUE ZN B 330
2AC2SOFTWAREHIS A:166 , HIS A:266 , HOH A:484 , HIS B:211BINDING SITE FOR RESIDUE ZN A 331
3AC3SOFTWAREHIS C:211 , HOH C:560 , HIS D:166 , HIS D:266BINDING SITE FOR RESIDUE ZN D 332
4AC4SOFTWAREHIS C:166 , HIS C:266 , HOH C:365 , HOH C:631 , HIS D:211BINDING SITE FOR RESIDUE ZN C 333

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PS7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:242 -Pro A:243
2Gly C:242 -Pro C:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PS7)

(-) Exons   (0, 0)

(no "Exon" information available for 1PS7)

(-) Sequences/Alignments

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:328
 aligned with PDXA_ECOLI | P19624 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:328
                                    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       321        
           PDXA_ECOLI     2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ 329
               SCOP domains d1ps7a_ A: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ps7A00 A:2-329 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhh......eeee..hhhhhhhhhhhhh...eeee.............eeee................hhhhhhhhhhhhhhhhhhhh....eee...hhhhhhhh.....hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...eeee..................eeeee.....eee.....hhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ps7 A   2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAmLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLNELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNTQ 329
                                    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       321  |     
                                                                          49-MSE                                                                                               151-MSE                                                            218-MSE             238-MSE                   264-MSE                                                     324-MSE 
                                                                                                                                                                                152-MSE                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with PDXA_ECOLI | P19624 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:328
                                    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       321        
           PDXA_ECOLI     2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ 329
               SCOP domains d1ps7b_ B: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ps7B00 B:2-329 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhh......eeeeeehhhhhhhhhhhhh...eeee.............eeeeee............hhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhh.....hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhh.....eeeee.....eeee...............hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ps7 B   2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAmLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLNELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNTQ 329
                                    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       321  |     
                                                                          49-MSE                                                                                               151-MSE                                                            218-MSE             238-MSE                   264-MSE                                                     324-MSE 
                                                                                                                                                                                152-MSE                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:328
 aligned with PDXA_ECOLI | P19624 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:328
                                    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       321        
           PDXA_ECOLI     2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ 329
               SCOP domains d1ps7c_ C: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ps7C00 C:2-329 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhh......eeeeeehhhhhhhhhhh.....eeee.............eeeeee............hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhh.....hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhh.....eeeee....eeee................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ps7 C   2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAmLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLNELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNTQ 329
                                    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       321  |     
                                                                          49-MSE                                                                                               151-MSE                                                            218-MSE             238-MSE                   264-MSE                                                     324-MSE 
                                                                                                                                                                                152-MSE                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:328
 aligned with PDXA_ECOLI | P19624 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:328
                                    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       321        
           PDXA_ECOLI     2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ 329
               SCOP domains d1ps7d_ D: 4-hydroxythreonine-4-phosphate dehydrogenase PdxA                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ps7D00 D:2-329 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) -----------------------PdxA-1ps7D01 D:25-322                                                                                                                                                                                                                                                                                     ------- Pfam domains (1)
           Pfam domains (2) -----------------------PdxA-1ps7D02 D:25-322                                                                                                                                                                                                                                                                                     ------- Pfam domains (2)
           Pfam domains (3) -----------------------PdxA-1ps7D03 D:25-322                                                                                                                                                                                                                                                                                     ------- Pfam domains (3)
           Pfam domains (4) -----------------------PdxA-1ps7D04 D:25-322                                                                                                                                                                                                                                                                                     ------- Pfam domains (4)
         Sec.struct. author ....eeeee......hhhhhhhhhh......eeee..hhhhhhhhhhhh....eeee.............eeee..............hhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhh.....hhhhhhhhhh.....eeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhh.....eeeee.....eee.....hhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ps7 D   2 VKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAmLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVmmLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHmGTEEIDTIIPVLNELRAQGmKLNGPLPADTLFQPKYLDNADAVLAmYHDQGLPVLKYQGFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKmIVNTQ 329
                                    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       321  |     
                                                                          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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PDXA_ECOLI | P19624)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.

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  1ps7
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  PDXA_ECOLI | P19624
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  1.1.1.262
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDXA_ECOLI | P19624: 1ps6 1ptm

(-) Related Entries Specified in the PDB File

1ps6 PDXA COMPLEXED WITH HTP
1ptm NATIVE HIGH RESOLUTION STRUCTURE