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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ASPARTATE RACEMASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  N. Maltseva, Y. Kim, K. Kwon, R. Zhang, W. F. Anderson, A. Joachimiak, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  27 May 11  (Deposition) - 15 Jun 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha Beta Fold, Racemase, Cytosol, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maltseva, Y. Kim, K. Kwon, R. Zhang, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Putative Aspartate Racemase From Salmonella Typhimurium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ASPARTATE RACEMASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: STM4510
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 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  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:11 , ARG A:49 , CYS A:83 , THR A:85 , THR A:124 , LYS A:163 , CL A:251 , HOH A:270 , HOH A:306BINDING SITE FOR RESIDUE SO4 A 250
02AC2SOFTWAREASN A:84 , THR A:85 , CYS A:193 , THR A:194 , SO4 A:250 , HOH A:306BINDING SITE FOR RESIDUE CL A 251
03AC3SOFTWAREALA A:201 , GLY A:202 , HIS A:203 , GLU A:204 , ARG A:205BINDING SITE FOR RESIDUE SO4 A 252
04AC4SOFTWARECYS A:31 , ASP A:32 , LYS B:163BINDING SITE FOR RESIDUE CL A 253
05AC5SOFTWAREMET B:11 , ARG B:49 , CYS B:83 , THR B:85 , THR B:124 , LYS B:163 , CL B:251 , HOH B:270 , HOH B:304 , HOH B:308BINDING SITE FOR RESIDUE SO4 B 250
06AC6SOFTWAREASN B:84 , THR B:85 , CYS B:193 , THR B:194 , SO4 B:250BINDING SITE FOR RESIDUE CL B 251
07AC7SOFTWAREALA B:201 , GLY B:202 , HIS B:203 , GLU B:204 , ARG B:205BINDING SITE FOR RESIDUE SO4 B 252
08AC8SOFTWAREARG A:184 , HOH A:302 , ARG B:62 , ARG B:66 , HOH B:657BINDING SITE FOR RESIDUE SO4 B 253
09AC9SOFTWAREMET C:11 , ARG C:49 , CYS C:83 , THR C:85 , THR C:124 , LYS C:163 , CL C:251 , HOH C:261 , HOH C:302 , HOH C:330BINDING SITE FOR RESIDUE SO4 C 250
10BC1SOFTWAREASN C:84 , THR C:85 , CYS C:193 , THR C:194 , SO4 C:250BINDING SITE FOR RESIDUE CL C 251
11BC2SOFTWAREALA C:201 , GLY C:202 , HIS C:203 , GLU C:204 , ARG C:205BINDING SITE FOR RESIDUE SO4 C 252
12BC3SOFTWAREARG C:62 , ARG C:66 , ARG D:184 , HOH D:338BINDING SITE FOR RESIDUE SO4 C 253
13BC4SOFTWAREMET D:11 , ARG D:49 , CYS D:83 , THR D:85 , THR D:124 , LYS D:163 , CL D:251 , HOH D:273 , HOH D:296BINDING SITE FOR RESIDUE SO4 D 250
14BC5SOFTWAREASN D:84 , THR D:85 , CYS D:193 , THR D:194 , SO4 D:250 , HOH D:273BINDING SITE FOR RESIDUE CL D 251
15BC6SOFTWAREGLY D:202 , HIS D:203 , GLU D:204 , ARG D:205BINDING SITE FOR RESIDUE SO4 D 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S81)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:11 -Gly A:12
2Met B:11 -Gly B:12
3Met C:11 -Gly C:12
4Met D:11 -Gly D:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S81)

(-) Exons   (0, 0)

(no "Exon" information available for 3S81)

(-) 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:232
 aligned with Q8ZJZ9_SALTY | Q8ZJZ9 from UniProtKB/TrEMBL  Length:244

    Alignment length:232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
         Q8ZJZ9_SALTY     1 MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDT 232
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhhhhhh...hhhhh..eeeee.....hhhhhhhhh...hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhh..ee.hhhhhhhhh......eeeee.hhhhhhh..hhhhhhhhh.eee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhh.hhhhh...eeehhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s81 A   1 MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDT 232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with Q8ZJZ9_SALTY | Q8ZJZ9 from UniProtKB/TrEMBL  Length:244

    Alignment length:240
                                   1                                                                                                                                                                                                                                        
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
         Q8ZJZ9_SALTY     - -------MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeee..hhhhhhhhhhhhhhhh...hhhhh..eeeee.....hhhhhhhhh...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhh..ee.hhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhh.hhhhh...eeehhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s81 B  -6 LYFQSNAMKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain C from PDB  Type:PROTEIN  Length:239
 aligned with Q8ZJZ9_SALTY | Q8ZJZ9 from UniProtKB/TrEMBL  Length:244

    Alignment length:239
                                  1                                                                                                                                                                                                                                        
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         
         Q8ZJZ9_SALTY     - ------MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..hhhhhhhhhhhhhhhh...hhhhh..eeeee.....hhhhhhhhh...hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhh..ee.hhhhhhhhh......eeeee.hhhhhhhh.hhhhhhhh..eee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhh.hhhhh...eeehhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s81 C  -5 YFQSNAMKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         


Chain D from PDB  Type:PROTEIN  Length:233
 aligned with Q8ZJZ9_SALTY | Q8ZJZ9 from UniProtKB/TrEMBL  Length:244

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
         Q8ZJZ9_SALTY     1 MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Asp_Glu_race-3s81D01 D:8-223                                                                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) -------Asp_Glu_race-3s81D02 D:8-223                                                                                                                                                                                            ---------- Pfam domains (2)
           Pfam domains (3) -------Asp_Glu_race-3s81D03 D:8-223                                                                                                                                                                                            ---------- Pfam domains (3)
           Pfam domains (4) -------Asp_Glu_race-3s81D04 D:8-223                                                                                                                                                                                            ---------- Pfam domains (4)
         Sec.struct. author ....eeee...hhhhhhhhhhhhhhhh...hhhhh..eeeee.....hhhhhhhhh...hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhh..ee.hhhhhhhhh......eeeee.hhhhhhh..hhhhhhhh..eee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhh.hhhhh...eeehhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s81 D   1 MKHTIGILGGMGPAATADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLLSGGPSPYRYLERYLHMLEDAGAECIVIPCNTAHYWFDDLQNVAKARMISILDATLGDIPPSARHVGLLATNATLATGLYQKKALARGLTLIQPEDAGQALVMQAIYTLKRGDKTAAQALLLPQIDSLIARGAQAIIMGCTEIPLIVAGHERAIACPMIDSTASLVRAAIRWYESWPDTR 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 3S81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S81)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Asp-glut_race (23)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8ZJZ9_SALTY | Q8ZJZ9)
molecular function
    GO:0047661    amino-acid racemase activity    Catalysis of the reaction: an L-amino acid = a D-amino acid.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0036361    racemase activity, acting on amino acids and derivatives    Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
    GO:0016855    racemase and epimerase activity, acting on amino acids and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
biological process
    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.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

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  3s81
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8ZJZ9_SALTY | Q8ZJZ9: 3s7z 5evc

(-) Related Entries Specified in the PDB File

3s7z THE SAME PROTEIN WITH LIGAND RELATED ID: IDP02135 RELATED DB: TARGETDB