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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE FROM YERSINIA PESTIS CO92
 
Authors :  B. Nocek, N. Maltseva, K. Kwon, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases
Date :  25 Feb 10  (Deposition) - 09 Mar 10  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  4-Hydroxythreonine-4-Phosphate Dehydrogenase, Pdxa, Nad-Dependent, Dehydrogenase, Metal-Binding, Nad, Nadp, Oxidoreductase, Pyridoxine Biosynthesis, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, N. Maltseva, K. Kwon, M. Makowska-Grzyska, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of 4-Hydroxythreonine-4-Phosphate Dehydrogenase From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.262
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PMCSG7
    Gene: PDXA, YPO0493, Y3682, YP_3686
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: 4-(PHOSPHOHYDROXY)-L-THREONINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO42Ligand/IonSULFATE ION
3SUC2Ligand/IonSUCROSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:167 , HIS A:212 , HIS A:267 , HOH A:345 , HOH A:463 , HOH A:467BINDING SITE FOR RESIDUE NI A 501
2AC2SOFTWAREGLY A:136 , HIS A:137 , THR A:138 , ASN A:284 , ARG A:293 , HOH A:421 , HOH A:519BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWAREARG A:58 , ILE A:67 , HIS A:212 , ALA A:213 , GLY A:216 , GLU A:223 , GLY A:243 , PRO A:244 , HOH A:395 , HOH A:452 , HOH A:490 , HOH A:510BINDING SITE FOR RESIDUE SUC A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LXY)

(-) Exons   (0, 0)

(no "Exon" information available for 3LXY)

(-) 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:329
 aligned with PDXA_YERPE | P58719 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:329
                                    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       280       290       300       310       320         
           PDXA_YERPE     1 MHNHNNRLVITPGEPAGVGPDLAITLAQQDWPVELVVCADPALLLARASQLNLPLQLREYQADQPAIAQQAGSLTILPVKTAVNVVPGKLDVGNSHYVVETLAKACDGAISGEFAALVTGPVQKSIINDAGIPFIGHTEFFADRSHCQRVVMMLATEELRVALATTHLPLLAVPGAITQASLHEVITILDNDLKTKFGITQPQIYVCGLNPHAGEGGHMGHEEIDTIIPALNTLRQQGINLIGPLPADTLFQPKYLQHADAVLAMYHDQGLPVLKYQGFGRAVNITLGLPFIRTSVDHGTALELAATGTADVGSFITALNLAIKMINNS 329
               SCOP domains d3lxya_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------PdxA-3lxyA01 A:25-323                                                                                                                                                                                                                                                                                      ------ Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhh......eeeeeehhhhhhhhhhhh....eeee.............eeeeee............hhhhhhhhhhhhhhhhhhhhhh....eee...hhhhhhhh.....hhhhhhhhhhh....eeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh...eeeee.....eeee....hhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxy A   1 MHNHNNRLVITPGEPAGVGPDLAITLAQQDWPVELVVCADPALLLARASQLNLPLQLREYQADQPAIAQQAGSLTILPVKTAVNVVPGKLDVGNSHYVVETLAKACDGAISGEFAALVTGPVQKSIINDAGIPFIGHTEFFADRSHCQRVVMMLATEELRVALATTHLPLLAVPGAITQASLHEVITILDNDLKTKFGITQPQIYVCGLNPHAGEGGHMGHEEIDTIIPALNTLRQQGINLIGPLPADTLFQPKYLQHADAVLAMYHDQGLPVLKYQGFGRAVNITLGLPFIRTSVDHGTALELAATGTADVGSFITALNLAIKMINNS 329
                                    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       280       290       300       310       320
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDXA_YERPE | P58719)
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.

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