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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DEOXYRIBOSE-PHOSPHATE ALDOLASE FROM ENTAMOEBA HISTOLYTICA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  11 Jun 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase, Deoxyribose-Phosphate Aldolase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, A. Gardberg, B. Staker
Crystal Structure Of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Gene: EHI_121800
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NA4Ligand/IonSODIUM ION
3ZN8Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:119 , GLY A:120 , ALA A:122 , HOH A:263 , HOH A:276 , HOH A:306BINDING SITE FOR RESIDUE NA A 249
02AC2SOFTWAREASP A:192 , HIS A:218 , HIS B:162 , HOH B:711BINDING SITE FOR RESIDUE ZN A 250
03AC3SOFTWARECYS A:40 , CYS A:61 , THR A:62 , ASP A:92BINDING SITE FOR RESIDUE ZN A 251
04AC4SOFTWARESER B:119 , GLY B:120 , ALA B:122 , HOH B:226 , HOH B:227 , HOH B:355BINDING SITE FOR RESIDUE NA B 249
05AC5SOFTWAREASP B:192 , HIS B:218 , HOH B:853 , HOH B:989BINDING SITE FOR RESIDUE ZN B 250
06AC6SOFTWARECYS B:40 , CYS B:61 , THR B:62 , ASP B:92BINDING SITE FOR RESIDUE ZN B 251
07AC7SOFTWARESER C:119 , GLY C:120 , ALA C:122 , HOH C:220 , HOH C:240 , HOH C:318BINDING SITE FOR RESIDUE NA C 249
08AC8SOFTWAREASP C:192 , HIS C:218 , HIS D:162 , HOH D:222BINDING SITE FOR RESIDUE ZN C 250
09AC9SOFTWARECYS C:40 , CYS C:61 , THR C:62 , ASP C:92BINDING SITE FOR RESIDUE ZN C 251
10BC1SOFTWARESER D:119 , GLY D:120 , ALA D:122 , HOH D:220 , HOH D:433 , HOH D:462BINDING SITE FOR RESIDUE NA D 249
11BC2SOFTWAREASP D:192 , HIS D:218 , HOH D:918BINDING SITE FOR RESIDUE ZN D 250
12BC3SOFTWARECYS D:40 , CYS D:61 , THR D:62 , ASP D:92BINDING SITE FOR RESIDUE ZN D 251
13BC4SOFTWARELYS B:103 , TYR B:105 , ASP B:106 , ARG B:144 , HOH B:366 , HOH B:451 , HOH B:588BINDING SITE FOR RESIDUE EDO B 252
14BC5SOFTWARETHR C:190 , PHE C:191 , ASP C:192 , ALA C:212 , GLY C:216 , HIS C:218 , HOH C:260BINDING SITE FOR RESIDUE EDO C 252
15BC6SOFTWAREASP C:192 , MET C:195 , LYS C:196 , HOH C:744 , HOH C:994 , THR D:161BINDING SITE FOR RESIDUE EDO C 219

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:61

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:66 -Pro A:67
2Phe B:66 -Pro B:67
3Phe C:66 -Pro C:67
4Phe D:66 -Pro D:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NGJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:218
 aligned with C4M5C6_ENTHI | C4M5C6 from UniProtKB/TrEMBL  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         C4M5C6_ENTHI     1 MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhheeeee....hhhhhhhhhhh.eeeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngj A   1 MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with C4M5C6_ENTHI | C4M5C6 from UniProtKB/TrEMBL  Length:218

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         C4M5C6_ENTHI     1 MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngj B   1 MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain C from PDB  Type:PROTEIN  Length:221
 aligned with C4M5C6_ENTHI | C4M5C6 from UniProtKB/TrEMBL  Length:218

    Alignment length:221
                               1                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 
         C4M5C6_ENTHI     - ---MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngj C  -2 PGSMDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 


Chain D from PDB  Type:PROTEIN  Length:222
 aligned with C4M5C6_ENTHI | C4M5C6 from UniProtKB/TrEMBL  Length:218

    Alignment length:222
                                1                                                                                                                                                                                                                         
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  
         C4M5C6_ENTHI     - ----MDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------DeoC-3ngjD01 D:5-216                                                                                                                                                                                                -- Pfam domains (1)
           Pfam domains (2) --------DeoC-3ngjD02 D:5-216                                                                                                                                                                                                -- Pfam domains (2)
           Pfam domains (3) --------DeoC-3ngjD03 D:5-216                                                                                                                                                                                                -- Pfam domains (3)
           Pfam domains (4) --------DeoC-3ngjD04 D:5-216                                                                                                                                                                                                -- Pfam domains (4)
         Sec.struct. author .....hhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhheeeee....hhhhhhhhhhh.eeeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngj D  -3 GPGSMDKATLAKYIDHTLLKADATEEQIRKLCSEAAEYKFASVCVNPTWVPLCAELLKGTGVKVCTVIGFPLGATPSEVKAYETKVAVEQGAEEVDMVINIGMVKAKKYDDVEKDVKAVVDASGKALTKVIIECCYLTNEEKVEVCKRCVAAGAEYVKTSTGFGTHGATPEDVKLMKDTVGDKALVKAAGGIRTFDDAMKMINNGASRIGASAGIAILNGIH 218
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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 3NGJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: DeoC (21)
(-)
Entamoeba histolytica (1)
1aDeoC-3ngjD01D:5-216
1bDeoC-3ngjD02D:5-216
1cDeoC-3ngjD03D:5-216
1dDeoC-3ngjD04D:5-216

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (C4M5C6_ENTHI | C4M5C6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004139    deoxyribose-phosphate aldolase activity    Catalysis of the reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0009264    deoxyribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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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