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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI KETOPANTOATE REDUCTASE IN A TERNARY COMPLEX WITH NADP+ AND PANTOATE
 
Authors :  A. Ciulli, D. Y. Chirgadze, A. G. Smith, T. L. Blundell, C. Abell
Date :  04 Jan 07  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pane, Apba, Ketopantoate Reductase, Ternary Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ciulli, D. Y. Chirgadze, A. G. Smith, T. L. Blundell, C. Abell
Crystal Structure Of Escherichia Coli Ketopantoate Reductase In A Ternary Complex With Nadp+ And Pantoate Bound: Substrate Recognition, Conformational Change, And Cooperativity.
J. Biol. Chem. V. 282 8487 2007
PubMed-ID: 17229734  |  Reference-DOI: 10.1074/JBC.M611171200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KETOPANTOATE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MINI-PRSETA
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PANE, APBA
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12
    Synonym: 2-DEHYDROPANTOATE 2-REDUCTASE, KPA REDUCTASE, KPR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4PAF2Ligand/IonPANTOATE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4PAF1Ligand/IonPANTOATE
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4PAF1Ligand/IonPANTOATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:171 , LEU B:227 , HOH B:946BINDING SITE FOR RESIDUE ACT B 801
2AC2SOFTWARELEU A:6 , GLY A:7 , GLY A:9 , ALA A:10 , LEU A:11 , TRP A:29 , LEU A:30 , ARG A:31 , THR A:70 , LEU A:71 , LYS A:72 , GLN A:75 , ALA A:79 , HIS A:97 , ASN A:98 , THR A:118 , HIS A:120 , ALA A:121 , ALA A:122 , GLU A:256 , HOH A:712 , HOH A:713 , HOH A:768 , HOH A:769 , HOH A:785 , HOH A:791 , HOH A:796 , HOH A:802 , HOH A:846 , HOH A:868 , HOH A:876BINDING SITE FOR RESIDUE NAP A 304
3AC3SOFTWARELEU B:6 , GLY B:7 , CYS B:8 , GLY B:9 , ALA B:10 , LEU B:11 , TRP B:29 , LEU B:30 , ARG B:31 , THR B:70 , LEU B:71 , LYS B:72 , GLN B:75 , HIS B:97 , ASN B:98 , THR B:118 , HIS B:120 , ALA B:121 , ALA B:122 , ASN B:241 , SER B:244 , ARG B:253 , GLU B:256 , PAF B:601 , HOH B:812 , HOH B:834 , HOH B:839 , HOH B:879 , HOH B:885 , HOH B:886 , HOH B:893 , HOH B:913 , HOH B:914 , HOH B:919 , HOH B:941 , HOH B:988 , HOH B:999BINDING SITE FOR RESIDUE NAP B 802
4AC4SOFTWAREASN B:98 , LYS B:176 , ASN B:180 , ILE B:183 , ASN B:184 , ASN B:194 , ASN B:241 , SER B:243 , SER B:244 , NAP B:802BINDING SITE FOR RESIDUE PAF B 601
5AC5SOFTWAREASN A:98 , ASN A:180 , ASN A:184 , ASN A:194 , VAL A:234 , SER A:243 , SER A:244 , HOH A:838 , HOH A:849 , HOH A:853BINDING SITE FOR RESIDUE PAF A 602
6AC6SOFTWAREASP A:258 , TYR A:259 , ARG A:266 , ASN B:127BINDING SITE FOR RESIDUE DIO A 701
7AC7SOFTWAREGLY A:262 , ARG A:266 , ARG A:269 , HOH A:731 , ASN B:127BINDING SITE FOR RESIDUE DIO A 702
8AC8SOFTWAREASP A:229 , GLN A:233 , LYS B:21 , GLU B:43 , ASP B:45 , SER B:47 , HOH B:869BINDING SITE FOR RESIDUE DIO B 703
9AC9SOFTWAREALA B:55 , ASP B:57 , TRP B:190 , GLU B:203 , ARG B:280BINDING SITE FOR RESIDUE DIO B 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:161 -Asp A:162
2Pro B:161 -Asp B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OFP)

(-) Exons   (0, 0)

(no "Exon" information available for 2OFP)

(-) 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:293
 aligned with PANE_ECOLI | P0A9J4 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:293
                             1                                                                                                                                                                                                                                                                                                   
                             |       9        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       289   
           PANE_ECOLI     - -MKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEY 292
               SCOP domains d2ofpa2 A:0-167 Ketopantoate reductase PanE                                                                                                                             d2ofpa1 A:168-292 Ketopantoate reductase PanE                                                                                 SCOP domains
               CATH domains 2ofpA01 A:0-167 NAD(P)-binding Rossmann-like Domain                                                                                                                     2ofpA02 A:168-290 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeee.......eeeeee.....eeeeee...hhhhhhh..eeee.....hhhhhhhhhh........eeee.....hhhhh......eeeeee..eeeee..eeeeee...eeeee.......hhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ofp A   0 SMKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEY 292
                                     9        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       289   


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with PANE_ECOLI | P0A9J4 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:294
                             1                                                                                                                                                                                                                                                                                                    
                             |       9        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       289    
           PANE_ECOLI     - -MKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEYE 293
               SCOP domains d2ofpb2 B:0-167 Ketopantoate reductase PanE                                                                                                                             d2ofpb1 B:168-293 Ketopantoate reductase PanE                                                                                  SCOP domains
               CATH domains 2ofpB01 B:0-167 NAD(P)-binding Rossmann-like Domain                                                                                                                     2ofpB02 B:168-290 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                --- CATH domains
           Pfam domains (1) ---ApbA-2ofpB01 B:3-144                                                                                                                          -----------------------ApbA_C-2ofpB03 B:168-289                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) ---ApbA-2ofpB02 B:3-144                                                                                                                          -----------------------ApbA_C-2ofpB04 B:168-289                                                                                                  ---- Pfam domains (2)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeee.......eeeeee.....eeeeee...hhhhhhh..eeee..hhhhhhhhhhhhh........eeee....hhhhhh......eeeeee..eeeee..eeeeee...eeeee.......hhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ofp B   0 SMKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEYE 293
                                     9        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       289
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: ApbA_C] (5)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PANE_ECOLI | P0A9J4)
molecular function
    GO:0008677    2-dehydropantoate 2-reductase activity    Catalysis of the reaction: (R)-pantoate + NADP(+) = 2-dehydropantoate + H(+) + NADPH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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.
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:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
    GO:0033317    pantothenate biosynthetic process from valine    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid, from other compounds, including valine.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PANE_ECOLI | P0A9J4: 1ks9 1yjq 1yon

(-) Related Entries Specified in the PDB File

1ks9 CRYSTAL STRUCTURE OF ESCHERICHIA COLI KETOPANTOATE REDUCTASE
1yjq CRYSTAL STRUCTURE OF KETOPANTOATE REDUCTASE IN COMPLEX WITH NADP+
1yon CRYSTAL STRUCTURE OF KETOPANTOATE REDUCTASE IN COMPLEX WITH 2-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE