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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM SURE AT 2.75 ANGSTROM RESOLUTION IN MONOCLINIC FORM
 
Authors :  P. Anju, H. S. Savithri, M. R. N. Murthy
Date :  26 Sep 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Mononucleotidase, Survival Protein, Stationary Phase, Sur E, Hydrolase, Phosphatase, Divalent Metal Ion, Nucleotide-Binding, Multifunctional Enzyme, Rossmann Fold, Metal-Binding, Domain Swapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pappachan, H. S. Savithri, M. R. N. Murthy
Structural And Functional Studies On A Mesophilic Stationary Phase Survival Protein (Sur E) From Salmonella Typhimurium
Febs J. V. 275 5855 2008
PubMed-ID: 19021761  |  Reference-DOI: 10.1111/J.1742-4658.2008.06715.X

(-) Compounds

Molecule 1 - MULTIFUNCTIONAL PROTEIN SUR E
    Chains: A, B, C, D
    EC Number: 3.1.3.5, 3.1.3.6, 3.1.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSBET-A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: 5'/3'-NUCLEOTIDASE, SURVIVAL PROTEIN, NUCLEOSIDE MONOPHOSPHATE PHOSPHOHYDROLASE, EXOPOLYPHOSPHATASE

 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:9 , SER A:39 , ASN A:92 , PO4 A:1255BINDING SITE FOR RESIDUE MG A1254
2AC2SOFTWAREASP B:8 , ASP B:9 , SER B:39 , ASN B:92BINDING SITE FOR RESIDUE MG B1254
3AC3SOFTWAREASP C:8 , ASP C:9 , SER C:39 , ASN C:92BINDING SITE FOR RESIDUE MG C1254
4AC4SOFTWAREASP D:8 , ASP D:9 , SER D:39 , ASN D:92 , PO4 D:1256BINDING SITE FOR RESIDUE MG D1254
5AC5SOFTWARELEU C:45 , GLU C:112 , TYR D:103 , ALA D:182 , GLY D:200 , PRO D:202BINDING SITE FOR RESIDUE GOL D1255
6AC6SOFTWAREASP D:8 , SER D:39 , GLY D:40 , ASN D:92 , ASN D:96 , SER D:104 , GLY D:105 , THR D:106 , MG D:1254BINDING SITE FOR RESIDUE PO4 D1256
7AC7SOFTWAREASP A:8 , SER A:39 , GLY A:40 , ASN A:92 , ASN A:96 , SER A:104 , GLY A:105 , THR A:106 , MG A:1254BINDING SITE FOR RESIDUE PO4 A1255

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V4O)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Arg A:81 -Pro A:82
2Arg B:81 -Pro B:82
3Arg C:81 -Pro C:82
4Gly C:90 -Ile C:91
5Arg D:81 -Pro D:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V4O)

(-) Exons   (0, 0)

(no "Exon" information available for 2V4O)

(-) 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:254
 aligned with SURE_SALTY | P66881 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           SURE_SALTY     - -MRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
               SCOP domains d2v4oa_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2v4oA00 A:0-253  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhh...eeeeeee.................eeee.....eeee..hhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhh........eeeeee...hhhhh.eeee....ee.....eeeee.....eeeee.....eee....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4o A   0 SMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with SURE_SALTY | P66881 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           SURE_SALTY     - -MRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
               SCOP domains d2v4ob_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2v4oB00 B:0-253  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhh...eeeeeee.................eeee.....eeee..hhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhh.eeee....ee......eeee.....eeee......eee....hhhhhhhhheeeeeee.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4o B   0 SMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    


Chain C from PDB  Type:PROTEIN  Length:254
 aligned with SURE_SALTY | P66881 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           SURE_SALTY     - -MRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
               SCOP domains d2v4oc_ C: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2v4oC00 C:0-253  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhh...eeeeeee.................eeee.....eeee..hhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhh..eee....ee.....eeeee.....eeeee.....eee....hhhhhhhh..eeeeee.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4o C   0 SMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    


Chain D from PDB  Type:PROTEIN  Length:258
 aligned with SURE_SALTY | P66881 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:258
                                 1                                                                                                                                                                                                                                                            
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
           SURE_SALTY     - -----MRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
               SCOP domains d2v4od_ D: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v4oD00 D:-4-253  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                             CATH domains
           Pfam domains (1) -----SurE-2v4oD01 D:1-184                                                                                                                                                                    --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----SurE-2v4oD02 D:1-184                                                                                                                                                                    --------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----SurE-2v4oD03 D:1-184                                                                                                                                                                    --------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----SurE-2v4oD04 D:1-184                                                                                                                                                                    --------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ......eeeee......hhhhhhhhhhhh...eeeeeee.................eeee.....eeee..hhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhh..eee....ee.....eeeee.....eeeee.....eee....hhhhhhhh..eeeee......hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v4o D  -4 HGMASMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW 253
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: SurE] (4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SURE_SALTY | P66881)
molecular function
    GO:0008254    3'-nucleotidase activity    Catalysis of the reaction: a 3'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0004309    exopolyphosphatase activity    Catalysis of the reaction: polyphosphate(n) + H2O = polyphosphate(n-1) + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008252    nucleotidase activity    Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
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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  2v4o
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  SURE_SALTY | P66881
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 Related Entries

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

UniProtKB/Swiss-Prot
        SURE_SALTY | P66881: 2v4n 4g9o 4gad 4ryt 4ryu 4xep 4xer 4xgb 4xgp 4xh8 4xj7

(-) Related Entries Specified in the PDB File

2v4n CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM SURE AT 1.7 ANGSTROM RESOLUTION IN ORTHORHOMBIC FORM