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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STATIONARY PHASE SURVIVAL PROTEIN SURE FROM THERMUS THERMOPHILUS HB8 COCRYSTALLIZED WITH MANGANESE AND AMP
 
Authors :  W. Iwasaki, K. Miki
Date :  26 Dec 06  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sure Protein, Cocrystal Structure With Manganese Ion And Amp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Iwasaki, K. Miki
Crystal Structure Of The Stationary Phase Survival Protein Sure With Metal Ion And Amp
J. Mol. Biol. V. 371 123 2007
PubMed-ID: 17561111  |  Reference-DOI: 10.1016/J.JMB.2007.05.007

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE SURE
    Chains: A, B, C, D
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: STATIONARY PHASE SURVIVAL PROTEIN SURE, NUCLEOSIDE 5'- MONOPHOSPHATE PHOSPHOHYDROLASE

 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
1GOL2Ligand/IonGLYCEROL
2MN4Ligand/IonMANGANESE (II) ION
3SO49Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:8 , ASP A:9 , ASN A:96 , HOH A:594 , GLU C:37BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWAREGLY A:102 , HIS A:103 , SER A:178 , VAL A:179 , ARG A:180 , TYR A:182 , ARG A:214 , HOH A:518BINDING SITE FOR RESIDUE SO4 A 401
03AC3SOFTWAREARG A:180BINDING SITE FOR RESIDUE SO4 A 402
04AC4SOFTWAREARG A:228 , LEU A:229 , ASP A:230 , HOH A:556 , HOH B:1522BINDING SITE FOR RESIDUE SO4 A 403
05AC5SOFTWARETHR A:235 , ARG A:236 , PRO A:239 , THR A:240 , HOH A:522 , GLU B:156BINDING SITE FOR RESIDUE SO4 A 404
06AC6SOFTWAREASP B:8 , ASP B:9 , ASN B:96BINDING SITE FOR RESIDUE MN B 1301
07AC7SOFTWAREGLY B:102 , HIS B:103 , SER B:178 , VAL B:179 , ARG B:180 , TYR B:182 , ARG B:214 , HOH B:1505BINDING SITE FOR RESIDUE SO4 B 1401
08AC8SOFTWAREARG B:180 , PRO B:204BINDING SITE FOR RESIDUE SO4 B 1402
09AC9SOFTWAREGLU A:37 , ASP C:8 , ASP C:9 , ASN C:96 , HOH C:2470BINDING SITE FOR RESIDUE MN C 2301
10BC1SOFTWAREGLY C:102 , HIS C:103 , SER C:178 , ARG C:180 , TYR C:182 , ARG C:214 , HOH C:2411BINDING SITE FOR RESIDUE SO4 C 2401
11BC2SOFTWAREASP D:8 , ASP D:9 , ASN D:96BINDING SITE FOR RESIDUE MN D 3301
12BC3SOFTWAREGLY D:102 , HIS D:103 , SER D:178 , ARG D:180 , TYR D:182 , ARG D:214 , HOH D:3431BINDING SITE FOR RESIDUE SO4 D 3401
13BC4SOFTWAREARG D:180 , HOH D:3457BINDING SITE FOR RESIDUE SO4 D 3402
14BC5SOFTWAREVAL A:29 , PHE A:30 , HIS A:64 , PRO A:66 , HOH A:524 , HOH A:568BINDING SITE FOR RESIDUE GOL A 501
15BC6SOFTWAREVAL B:29 , PRO B:55 , HIS B:64 , PHE B:65 , PRO B:66 , HOH B:1520 , HOH B:1531BINDING SITE FOR RESIDUE GOL B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E6C)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:86 -Pro A:87
2Gly A:94 -Val A:95
3Arg A:157 -Pro A:158
4Gly B:86 -Pro B:87
5Gly B:94 -Val B:95
6Arg B:157 -Pro B:158
7Gly C:86 -Pro C:87
8Gly C:94 -Val C:95
9Arg C:157 -Pro C:158
10Gly D:86 -Pro D:87
11Gly D:94 -Val D:95
12Arg D:157 -Pro D:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E6C)

(-) Exons   (0, 0)

(no "Exon" information available for 2E6C)

(-) 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:243
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
               SCOP domains d2e6ca_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 2e6cA00 A:1-243  [code=3.40.1210.10, no name defined]                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee.................eeee...........eeeee.hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6c A   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
               SCOP domains d2e6cb_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 2e6cB00 B:1-243  [code=3.40.1210.10,       no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee..------..........eee...........eeee..hhhhhhhhhhhhhh...eeeeeeee...hhhhh..hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6c B   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
                                    10        20        30     |   -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                              36     43                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQ 238
               SCOP domains d2e6cc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2e6cC00 C:1-238  [code=3.40.1210.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee.................eeee...........eeeee.hhhhhhhhhhhhh....eeeeeeee...hhhhhh.hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee.......eee.......ee..eeeee.....eeeee..ee.......hhhhhhhh..eeeee......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6c C   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain D from PDB  Type:PROTEIN  Length:234
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPT 240
               SCOP domains d2e6cd_ D: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2e6cD00 D:1-240  [code=3.40.1210.10,       no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee..------..........eee...........eeee..hhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2e6c D   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPT 240
                                    10        20        30     |   -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
                                                              36     43
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E6C)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SURE_THET8 | Q53W92)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + 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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  2e6c
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 Related Entries

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

UniProtKB/Swiss-Prot
        SURE_THET8 | Q53W92: 2e69 2e6b 2e6e 2e6g 2e6h

(-) Related Entries Specified in the PDB File

1ilv SURE FROM THERMATOGA MARITIMA
1j9j SURE FROM THERMATOGA MARITIMA
1j9k SURE FROM THERMATOGA MARITIMA COMPLEXED WITH CALCIUM AND TUNGSTATE.
1j9l SURE FROM THERMATOGA MARITIMA COMPLEXED WITH CALCIUM AND VANADATE.
1l5x SURE HOMOLOG FROM PYROBACULUM AEROPHILUM
2e69 SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH SULFATE.
2e6b SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH MAGNESIUM AND TUNGSTATE.
2e6e SURE FROM THERMUS THERMOPHILUS HB8.
2e6g SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH PHOSPHATE.
2e6h E37A MUTANT OF SURE FROM THERMUS THERMOPHILUS HB8 COCRYSTALLIZED WITH MANGANESE AND AMP.