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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOMETHIONINE INCORPORATED APO D-SERINE DEAMINASE FROM SALMONELLA TYHIMURIUM
 
Authors :  S. R. Bharath, B. Shveta, H. S. Savithri, M. R. N. Murthy
Date :  09 Mar 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Foldtype 2 Of Plp-Dependent Enzymes, Alpha, Beta Elimination Of D- Serine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Bharath, S. Bisht, H. S. Savithri, M. R. N. Murthy
Crystal Structures Of Open And Closed Forms Of D-Serine Deaminase From Salmonella Typhimurium - Implications On Substrate Specificity And Catalysis
Febs J. 2011
PubMed-ID: 21668644  |  Reference-DOI: 10.1111/J.1742-4658.2011.08210.X

(-) Compounds

Molecule 1 - D-SERINE DEHYDRATASE
    Chains: A
    EC Number: 4.3.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B(+)
    Expression System Strain: BL21(DE3)ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DSDA, STM3802
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Synonym: D-SERINE DEAMINASE, DSD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MSE13Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:238 , SER A:239 , ARG A:240 , THR A:241 , HOH A:485 , HOH A:777 , HOH A:789BINDING SITE FOR RESIDUE SO4 A 449
2AC2SOFTWAREASN A:98 , GLY A:99 , GLY A:413 , HOH A:458 , HOH A:760 , HOH A:787BINDING SITE FOR RESIDUE SO4 A 450
3AC3SOFTWARETYR A:11BINDING SITE FOR RESIDUE EDO A 451
4AC4SOFTWAREALA A:390 , ARG A:394 , HOH A:482BINDING SITE FOR RESIDUE EDO A 452
5AC5SOFTWAREASN A:27 , GLY A:29 , GLU A:352 , ARG A:353 , HOH A:578BINDING SITE FOR RESIDUE EDO A 453
6AC6SOFTWARECYS A:276 , GLY A:277 , GLU A:303 , SER A:307 , CYS A:309 , LEU A:338 , VAL A:340BINDING SITE FOR RESIDUE NA A 454
7AC7SOFTWARELYS A:116 , GLY A:277 , VAL A:278 , GLY A:279 , GLY A:280 , GLY A:281 , PRO A:282 , HOH A:831 , HOH A:835 , HOH A:841BINDING SITE FOR RESIDUE SO4 A 455
8AC8SOFTWAREHIS A:51BINDING SITE FOR RESIDUE EDO A 456
9AC9SOFTWARELYS A:116 , SER A:165 , THR A:166 , GLY A:167 , ASN A:168 , LEU A:169 , ASP A:236 , HOH A:834 , HOH A:841BINDING SITE FOR RESIDUE EDO A 457

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R0X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R0X)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.SDHD_SALTY106-120  1A:106-120

(-) Exons   (0, 0)

(no "Exon" information available for 3R0X)

(-) 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:438
 aligned with SDHD_SALTY | Q8ZL08 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:438
                                    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       330       340       350       360       370       380       390       400       410       420       430        
           SDHD_SALTY     1 MENIQKLIARYPLVEDLVALKETTWFNPGATSLAQGLPYVGLTEQDVNAAHDRLARFAPYLAKAFPQTAAAGGMIESDVVAIPAMQKRLEKEYGQTINGEMLLKKDSHLAISGSIKARGGIYEVLTHAEKLALEAGLLTTDDDYSVLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSACIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEDDYGVAVEQGRKAAQSDPNCFFIDDENSRTLFLGYAVAGQRLKAQFAQQGRVVDASHPLFVYLPCGVGGGPGGVAFGLKLAFGDNVHCFFAEPTHSPCMLLGVYTGLHDAISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGLYTLDDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRICASVAYQQRHGFSQTQLGNATHLVWATGGGMVPEDEMEQYLAK 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------PALP-3r0xA01 A:80-407                                                                                                                                                                                                                                                                                                                   ------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..hhhhhhhh....eee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhh.hhhhh......hhhhh.....hhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..eeeeee......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------DEHYDRATASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r0x A   1 mENIQKLIARYPLVEDLVALKETTWFNPGATSLAQGLPYVGLTEQDVNAAHDRLARFAPYLAKAFPQTAAAGGmIESDVVAIPAmQKRLEKEYGQTINGEmLLKKDSHLAISGSIKARGGIYEVLTHAEKLALEAGLLTTDDDYSVLLSPEFKQFFSQYSIAVGSTGNLGLSIGImSACIGFKVTVHmSADARAWKKAKLRSHGVTVVEYEDDYGVAVEQGRKAAQSDPNCFFIDDENSRTLFLGYAVAGQRLKAQFAQQGRVVDASHPLFVYLPCGVGGGPGGVAFGLKLAFGDNVHCFFAEPTHSPCmLLGVYTGLHDAISVQDIGIDNLTAADGLAVGRASGFVGRAmERLLDGLYTLDDQTmYDmLGWLAQEEGIRLEPSALAGmAGPQRICASVAYQQRHGFSQTQLGNATHLVWATGGGmVPEDEmEQYLAK 438
                            |       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       330       340       350|      360     | 370       380       390       400       410       420     | 430 |      
                            |                                                                       74-MSE     85-MSE         101-MSE                                                                    176-MSE     188-MSE                                                                                                                   310-MSE                                  351-MSE        366-MSE                389-MSE                              426-MSE |      
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                         369-MSE                                                        432-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  (0, 0)

(no "SCOP Domain" information available for 3R0X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R0X)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PALP] (67)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SDHD_SALTY | Q8ZL08)
molecular function
    GO:0008721    D-serine ammonia-lyase activity    Catalysis of the reaction: D-serine = pyruvate + NH3.
    GO:0003941    L-serine ammonia-lyase activity    Catalysis of the reaction: L-serine = pyruvate + NH3.
    GO:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    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:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0030378    serine racemase activity    Catalysis of the synthesis of free D-serine from L-serine.
biological process
    GO:0046416    D-amino acid metabolic process    The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
    GO:0070179    D-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid. D-serine is often formed by racemization of L-serine.
    GO:0036088    D-serine catabolic process    The chemical reactions and pathways resulting in the breakdown of D-serine, the D-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
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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3r0z