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(-) Description

Title :  CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_1559) FROM THERMOTOGA MARITIMA AT 1.83 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Mar 11  (Deposition) - 30 Mar 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Beta/Alpha-Barrel, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Deoxyribose-Phosphate Aldolase (Tm_1559) From Thermotoga Maritima At 1. 83 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MH1
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DEOC, TM1559, TM_1559
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: PHOSPHODEOXYRIBOALDOLASE, DERA, DEOXYRIBOALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE
4UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:13 , ARG A:14 , TYR A:17BINDING SITE FOR RESIDUE ACT A 301
2AC2SOFTWARETYR A:157BINDING SITE FOR RESIDUE ACT A 302
3AC3SOFTWAREILE A:200BINDING SITE FOR RESIDUE ACT A 306
4AC4SOFTWAREGLY A:212 , ILE A:213 , ARG A:214 , THR A:232 , SER A:233 , SER A:234 , HOH A:320 , HOH A:400BINDING SITE FOR RESIDUE GOL A 307
5AC5SOFTWARECYS B:69BINDING SITE FOR RESIDUE ACT B 303
6AC6SOFTWAREARG B:14 , GLU B:161BINDING SITE FOR RESIDUE ACT B 304
7AC7SOFTWAREGLY B:187 , GLY B:188BINDING SITE FOR RESIDUE ACT B 305
8AC8SOFTWAREILE B:213 , ARG B:214 , THR B:232 , SER B:233 , SER B:234 , HOH B:331 , HOH B:420BINDING SITE FOR RESIDUE GOL B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R13)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:91 -Pro A:92
2Phe B:91 -Pro B:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R13)

(-) Exons   (0, 0)

(no "Exon" information available for 3R13)

(-) 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:257
 aligned with DEOC_THEMA | Q9X1P5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:257
                                      1                                                                                                                                                                                                                                                      
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           DEOC_THEMA     - ----------MIEYRIEEAVAKYREFYEFKPVRESAGIEDVKSAIEHTNLKPFATPDDIKKLCLEARENRFHGVCVNPCYVKLAREELEGTDVKVVTVVGFPLGANETRTKAHEAIFAVESGADEIDMVINVGMLKAKEWEYVYEDIRSVVESVKGKVVKVIIETCYLDTEEKIAACVISKLAGAHFVKTSTGFGTGGATAEDVHLMKWIVGDEMGVKASGGIRTFEDAVKMIMYGADRIGTSSGVKIVQGGEERYG 247
               SCOP domains d3r13a_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhheeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r13 A  -9 SDKIHHHHHHmIEYRIEEAVAKYREFYEFKPVRESAGIEDVKSAIEHTNLKPFATPDDIKKLCLEARENRFHGVCVNPCYVKLAREELEGTDVKVVTVVGFPLGANETRTKAHEAIFAVESGADEIDmVINVGmLKAKEWEYVYEDIRSVVESVKGKVVKVIIETCYLDTEEKIAACVISKLAGAHFVKTSTGFGTGGATAEDVHLmKWIVGDEmGVKASGGIRTFEDAVKmImYGADRIGTSSGVKIVQGGEERYG 247
                                     0|       10        20        30        40        50        60        70        80        90       100       110       120   |   130       140       150       160       170       180       190      |200    |  210       220 | |   230       240       
                                      1-MSE                                                                                                              118-MSE |                                                                      197-MSE 205-MSE          222-MSE                     
                                                                                                                                                               124-MSE                                                                                             224-MSE                   


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with DEOC_THEMA | Q9X1P5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:258
                                      1                                                                                                                                                                                                                                                       
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           DEOC_THEMA     - ----------MIEYRIEEAVAKYREFYEFKPVRESAGIEDVKSAIEHTNLKPFATPDDIKKLCLEARENRFHGVCVNPCYVKLAREELEGTDVKVVTVVGFPLGANETRTKAHEAIFAVESGADEIDMVINVGMLKAKEWEYVYEDIRSVVESVKGKVVKVIIETCYLDTEEKIAACVISKLAGAHFVKTSTGFGTGGATAEDVHLMKWIVGDEMGVKASGGIRTFEDAVKMIMYGADRIGTSSGVKIVQGGEERYGG 248
               SCOP domains d3r13b_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------DeoC-3r13B01 B:30-241                                                                                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------DeoC-3r13B02 B:30-241                                                                                                                                                                                               ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhheeeee.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r13 B  -9 SDKIHHHHHHmIEYRIEEAVAKYREFYEFKPVRESAGIEDVKSAIEHTNLKPFATPDDIKKLCLEARENRFHGVCVNPCYVKLAREELEGTDVKVVTVVGFPLGANETRTKAHEAIFAVESGADEIDmVINVGmLKAKEWEYVYEDIRSVVESVKGKVVKVIIETCYLDTEEKIAACVISKLAGAHFVKTSTGFGTGGATAEDVHLmKWIVGDEmGVKASGGIRTFEDAVKmImYGADRIGTSSGVKIVQGGEERYGG 248
                                     0|       10        20        30        40        50        60        70        80        90       100       110       120   |   130       140       150       160       170       180       190      |200    |  210       220 | |   230       240        
                                      1-MSE                                                                                                              118-MSE |                                                                      197-MSE 205-MSE          222-MSE                      
                                                                                                                                                               124-MSE                                                                                             224-MSE
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R13)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: DeoC (21)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEOC_THEMA | Q9X1P5)
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.
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.
    GO:0046386    deoxyribose phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose.
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

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UniProtKB/Swiss-Prot
        DEOC_THEMA | Q9X1P5: 3r12

(-) Related Entries Specified in the PDB File

3r12 CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_ 1559) FROM THERMOTOGA MARITIMA AT 1.75 A RESOLUTION (APO FORM)