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(-) Description

Title :  CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH PROLINE BETAINE
 
Authors :  A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Date :  30 Mar 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Binding-Protein, Compatible Solutes, Cation-Pi Interactions, Non- Classical Hydrogen Bonds, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Structural Basis For The Binding Of Compatible Solutes By Prox From The Hyperthermophilic Archaeon Archaeoglobus Fulgidus.
J. Biol. Chem. V. 279 48270 2004
PubMed-ID: 15308642  |  Reference-DOI: 10.1074/JBC.M403540200

(-) Compounds

Molecule 1 - OSMOPROTECTION PROTEIN (PROX)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA6
    Expression System Strain: BL21(CODON PLUS RIL)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PROX
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PBE2Ligand/Ion1,1-DIMETHYL-PROLINIUM
3ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2PBE1Ligand/Ion1,1-DIMETHYL-PROLINIUM
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2PBE1Ligand/Ion1,1-DIMETHYL-PROLINIUM
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:238 , ASP A:239 , GLU B:238 , ASP B:239BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:242 , ASP A:244 , HOH A:441 , ASP B:81BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREASP A:81 , ASP B:242 , ASP B:244 , HOH B:454BINDING SITE FOR RESIDUE ZN B 403
4AC4SOFTWAREASP A:136 , HOH A:490 , HOH A:503 , HOH A:519BINDING SITE FOR RESIDUE ZN A 404
5AC5SOFTWAREASP B:136 , HOH B:421 , HOH B:423 , HOH B:450BINDING SITE FOR RESIDUE ZN B 405
6AC6SOFTWARELYS A:275 , HOH A:448 , HOH A:449BINDING SITE FOR RESIDUE ZN A 406
7AC7SOFTWARELYS A:13 , PHE A:15 , TYR A:63 , THR A:66 , ASP A:109 , TYR A:111 , ARG A:149 , TYR A:190 , TYR A:214BINDING SITE FOR RESIDUE PBE A 301
8AC8SOFTWARELYS B:13 , PHE B:15 , TYR B:63 , THR B:66 , ASP B:109 , TYR B:111 , ARG B:149 , TYR B:190 , TYR B:214BINDING SITE FOR RESIDUE PBE B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SW1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SW1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SW1)

(-) Exons   (0, 0)

(no "Exon" information available for 1SW1)

(-) 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:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw1a_ A: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw1A01 A:6-109,A:214-275 Periplasmic binding protein-like II                                           1sw1A02 A:110-213 Osmoprotection protein (prox); domain 2                                               1sw1A01 A:6-109,A:214-275 Periplasmic binding protein-like II  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhhh..hhhhhh.hhhh.eeee.........hhhhhhhhhh....eeee.hhhhhhhhhhh.....eeee...hhhhhh.eee...........eeeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw1 A   6 ERVVIGSKPFNEQYILANmIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQmEPTLmYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTmRALNYQYDVEKKDAREIAmSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    |  175       185       195       205       215       225       235       245|      255       265       275
                                             24-MSE                                                                                                                                           170-MSE|                                                                    246-MSE            265-MSE      
                                                                                                                                                                                                   175-MSE                                                                                                


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw1b_ B: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw1B01 B:6-109,B:214-275 Periplasmic binding protein-like II                                           1sw1B02 B:110-213 Osmoprotection protein (prox); domain 2                                               1sw1B01 B:6-109,B:214-275 Periplasmic binding protein-like II  CATH domains
           Pfam domains (1) OpuAC-1sw1B01 B:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) OpuAC-1sw1B02 B:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhhh..hhhhhh.hhhh.eeee.........hhhhhhhhhh....eeee.hhhhhhhhhhh.....eeee...hhhhhh.eee...........eeeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw1 B   6 ERVVIGSKPFNEQYILANmIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQmEPTLmYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTmRALNYQYDVEKKDAREIAmSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    |  175       185       195       205       215       225       235       245|      255       265       275
                                             24-MSE                                                                                                                                           170-MSE|                                                                    246-MSE            265-MSE      
                                                                                                                                                                                                   175-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O29280_ARCFU | O29280)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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 Related Entries

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        O29280_ARCFU | O29280: 1sw2 1sw4 1sw5 3mam

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