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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDROPANTOATE 2-REDUCTASE FROM GEOBACTER METALLIREDUCENS GS-15
 
Authors :  Y. Patskovsky, R. Toro, C. Morano, M. Rutter, S. Chang, J. M. Sauder, S. K S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)
Date :  29 May 09  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  2-Dehydropantoate 2-Reductase, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nadp, Oxidoreductase, Pantothenate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, C. Morano, M. Rutter, S. Chang, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of 2-Dehydropantoate 2-Reductase From Geobacter Metallireducens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-DEHYDROPANTOATE 2-REDUCTASE
    Atcc: 53774
    Chains: A, B, C, D
    EC Number: 1.1.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GMET_2643
    Organism Scientific: GEOBACTER METALLIREDUCENS
    Organism Taxid: 269799
    Strain: GS-15

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HN2)

(-) Sites  (0, 0)

(no "Site" information available for 3HN2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HN2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HN2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HN2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HN2)

(-) Exons   (0, 0)

(no "Exon" information available for 3HN2)

(-) 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:302
 aligned with Q39SB2_GEOMG | Q39SB2 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                                                                                                                                                                                                                                                                                                                      302 
                                    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| 
         Q39SB2_GEOMG     2 RIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATG-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhh...eeee...hhhhhhhh.eeeee....eee....ee.hhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh.eeeeeeeee.......eeee.eeeeeeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn2 A   2 RIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATGE 303
                                    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  


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q39SB2_GEOMG | Q39SB2 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    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  
         Q39SB2_GEOMG     1 MRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATG 302
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh..eeeee....hhhhhh..eeee.....eee....ee.hhhhhh...eeee..hhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhh.eeeeeeeeeeee....eeeeeeeeeeeeee....hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn2 B   1 LRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATG 302
                                    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  


Chain C from PDB  Type:PROTEIN  Length:302
 aligned with Q39SB2_GEOMG | Q39SB2 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    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  
         Q39SB2_GEOMG     1 MRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATG 302
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee...hhhhhh...eeee.....eee....ee.hhhhh....eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh...eeeeeeeeeeeeee..eeeeeeeeeeeeee.....hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn2 C   1 LRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQATG 302
                                    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  


Chain D from PDB  Type:PROTEIN  Length:301
 aligned with Q39SB2_GEOMG | Q39SB2 from UniProtKB/TrEMBL  Length:302

    Alignment length:301
                                    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 
         Q39SB2_GEOMG     1 MRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQAT 301
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh..eeeee....hhhhhh..eeee....eeee...eee.hhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeeeeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hn2 D   1 LRIAIVGAGALGLYYGALLQRSGEDVHFLLRRDYEAIAGNGLKVFSINGDFTLPHVKGYRAPEEIGPMDLVLVGLKTFANSRYEELIRPLVEEGTQILTLQNGLGNEEALATLFGAERIIGGVAFLCSNRGEPGEVHHLGAGRIILGEFLPRDTGRIEELAAMFRQAGVDCRTTDDLKRARWEKLVWNIPFNGLCALLQQPVNLILARDVSRKLVRGIMLEVIAGANAQGLATFIADGYVDDMLEFTDAMGEYKPSMEIDREEGRPLEIAAIFRTPLAYGAREGIAMPRVEMLATLLEQAT 301
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3HN2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HN2)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q39SB2_GEOMG | Q39SB2)
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.
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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  3hn2
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