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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH
 
Authors :  G. Sulzenbacher, V. Roig-Zamboni, F. Pagot, S. Grisel, A. Salamoni, C. Valencia, C. Bignon, R. Vincentelli, M. Tegoni, C. Cambillau
Date :  26 Nov 02  (Deposition) - 21 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Unknown Function, Possible Nadph-Dependent Quinone Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sulzenbacher, V. Roig-Zamboni, F. Pagot, S. Grisel, A. Salomoni, C. Valencia, V. Campanacci, R. Vincentelli, M. Tegoni, H. Eklund, C. Cambillau
Structure Of Escherichia Coli Yhdh, A Putative Quinone Oxidoreductase
Acta Crystallogr. , Sect. D V. 60 1855 2004
PubMed-ID: 15388933  |  Reference-DOI: 10.1107/S0907444904020220

(-) Compounds

Molecule 1 - YHDH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PDEST17
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: B3253, YHDH, PUTATIVE QUINONE OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:41 , THR A:126 , THR A:130 , GLY A:154 , SER A:156 , GLY A:157 , GLY A:158 , VAL A:159 , SER A:178 , GLY A:179 , ARG A:180 , ARG A:198 , THR A:218 , CYS A:240 , GLY A:241 , LEU A:242 , ALA A:243 , GLY A:244 , ASP A:266 , SER A:267 , VAL A:268 , ILE A:310 , ASN A:313 , HOH A:2051 , HOH A:2114 , HOH A:2115 , HOH A:2116 , HOH A:2117 , HOH A:2118 , ILE D:256BINDING SITE FOR RESIDUE NDP A1325
2AC2SOFTWARETYR B:41 , THR B:126 , THR B:130 , GLY B:154 , SER B:156 , GLY B:157 , GLY B:158 , VAL B:159 , SER B:178 , GLY B:179 , ARG B:180 , ARG B:198 , THR B:218 , CYS B:240 , GLY B:241 , LEU B:242 , ALA B:243 , GLY B:244 , ASP B:266 , SER B:267 , VAL B:268 , ILE B:310 , ASN B:313 , ILE B:315 , HOH B:2071 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075 , ILE C:256BINDING SITE FOR RESIDUE NDP B1325
3AC3SOFTWAREILE B:256 , TYR C:41 , THR C:126 , THR C:130 , GLY C:154 , SER C:156 , GLY C:157 , GLY C:158 , VAL C:159 , SER C:178 , GLY C:179 , ARG C:180 , ARG C:198 , THR C:218 , VAL C:219 , CYS C:240 , GLY C:241 , LEU C:242 , ALA C:243 , GLY C:244 , ASP C:266 , SER C:267 , VAL C:268 , ILE C:310 , ASN C:313 , HOH C:2086 , HOH C:2091 , HOH C:2092 , HOH C:2093 , HOH C:2094 , HOH C:2095BINDING SITE FOR RESIDUE NDP C1325
4AC4SOFTWAREILE A:256 , TYR D:41 , THR D:126 , THR D:130 , GLY D:154 , SER D:156 , GLY D:157 , GLY D:158 , VAL D:159 , SER D:178 , GLY D:179 , ARG D:180 , ARG D:198 , THR D:218 , VAL D:219 , CYS D:240 , GLY D:241 , LEU D:242 , ALA D:243 , GLY D:244 , ASP D:266 , SER D:267 , VAL D:268 , ILE D:310 , ASN D:313 , ILE D:315 , HOH D:2032 , HOH D:2038 , HOH D:2055 , HOH D:2058 , HOH D:2059 , HOH D:2060BINDING SITE FOR RESIDUE NDP D1325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O8C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:57 -Pro A:58
2Phe B:57 -Pro B:58
3Phe C:57 -Pro C:58
4Phe D:57 -Pro D:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O8C)

(-) Exons   (0, 0)

(no "Exon" information available for 1O8C)

(-) 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:324
 aligned with ACUI_ECOLI | P26646 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:324
                                    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    
           ACUI_ECOLI     1 MQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
               SCOP domains d1o8ca3 A:1-115,A:293-323 Hypothetical protein YhdH                                                                d1o8ca4 A:116-292 Hypothetical protein YhdH                                                                                                                                      d1o8ca3 A:1-115,A:293-323      - SCOP domains
               CATH domains 1o8cA01 A:1-124,A:292-324 Medium-chain alcohol dehydrogenases, catalytic domain                                             1o8cA02 A:125-291 NAD(P)-binding Rossmann-like Domain                                                                                                                  1o8cA01 A:1-124,A:292-324         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee.hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhheeee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhheeeeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o8c A   1 LQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
                                    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    


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with ACUI_ECOLI | P26646 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:324
                                    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    
           ACUI_ECOLI     1 MQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
               SCOP domains d1o8cb3 B:1-115,B:293-323 Hypothetical protein YhdH                                                                d1o8cb4 B:116-292 Hypothetical protein YhdH                                                                                                                                      d1o8cb3 B:1-115,B:293-323      - SCOP domains
               CATH domains 1o8cB01 B:1-124,B:292-324 Medium-chain alcohol dehydrogenases, catalytic domain                                             1o8cB02 B:125-291 NAD(P)-binding Rossmann-like Domain                                                                                                                  1o8cB01 B:1-124,B:292-324         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee.hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o8c B   1 LQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
                                    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    


Chain C from PDB  Type:PROTEIN  Length:323
 aligned with ACUI_ECOLI | P26646 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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   
           ACUI_ECOLI     2 QALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
               SCOP domains d1o8cc1 C:2-115,C:293-323 Hypothetical protein YhdH                                                               d1o8cc3 C:116-292 Hypothetical protein YhdH                                                                                                                                      d1o8cc1 C:2-115,C:293-323      - SCOP domains
               CATH domains 1o8cC01 C:2-124,C:292-324 Medium-chain alcohol dehydrogenases, catalytic domain                                            1o8cC02 C:125-291 NAD(P)-binding Rossmann-like Domain                                                                                                                  1o8cC01 C:2-124,C:292-324         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee..hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o8c C   2 QALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
                                    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   


Chain D from PDB  Type:PROTEIN  Length:324
 aligned with ACUI_ECOLI | P26646 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:324
                                    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    
           ACUI_ECOLI     1 MQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
               SCOP domains d1o8cd3 D:1-115,D:293-323 Hypothetical protein YhdH                                                                d1o8cd4 D:116-292 Hypothetical protein YhdH                                                                                                                                      d1o8cd3 D:1-115,D:293-323      - SCOP domains
               CATH domains 1o8cD01 D:1-124,D:292-324 Medium-chain alcohol dehydrogenases, catalytic domain                                             1o8cD02 D:125-291 NAD(P)-binding Rossmann-like Domain                                                                                                                  1o8cD01 D:1-124,D:292-324         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee.hhhhh....eeeeeeeeeehhhhhhhhhh..............eeeeeeeee.........eeeee..............eeeehhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee.hhh..........eeeeee..hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhhh.eeee......hhhhhhhhhhhhhhhh.hhhhhhheeeee..hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o8c D   1 LQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN 324
                                    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
   Legend:   → Mismatch (orange background)
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  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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O8C)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ACUI_ECOLI | P26646)
molecular function
    GO:0043957    acryloyl-CoA reductase (NADP+) activity    Catalysis of the reaction: acryloyl-CoA + NADPH + H+ = propionyl-CoA + NADP+.
    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: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.
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
        ACUI_ECOLI | P26646: 1o89

(-) Related Entries Specified in the PDB File

1o89 STRUCTURAL GENOMICS, UNKNOWN FUNCTION, CRYSTAL STRUCTURE OF E. COLI K-12 YHDH