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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL NIL DOMAIN OF AN ABC TRANSPORTER PROTEIN HOMOLOGUE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  M. E. Cuff, L. Bigelow, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  28 Feb 08  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Abc Transporter, Nil Domain, Staphylococcus Aureus, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Amino-Acid Transport, Atp-Binding, Hydrolase, Membrane, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Cuff, L. Bigelow, S. Clancy, A. Joachimiak
The Structure Of The C-Terminal Nil Domain Of An Abc Transporter Protein Homologue From Staphylococcus Aureus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE IMPORT ATP-BINDING PROTEIN METN 2
    Atcc700699
    ChainsA, B, C
    EC Number3.6.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMETN2, SAV0837
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid158878
    StrainMU50

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BU14Ligand/Ion1,4-BUTANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BU1-1Ligand/Ion1,4-BUTANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA C:286 , ASP C:320BINDING SITE FOR RESIDUE BU1 C 401
2AC2SOFTWAREASP A:320 , ASP B:320BINDING SITE FOR RESIDUE BU1 A 402
3AC3SOFTWAREASN A:292 , HIS A:312BINDING SITE FOR RESIDUE BU1 A 403
4AC4SOFTWAREGLU C:260 , ASN C:292 , HIS C:312BINDING SITE FOR RESIDUE BU1 C 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:257 -Pro A:258
2Glu B:257 -Pro B:258
3Glu C:257 -Pro C:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CED)

(-) 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:98
 aligned with METN2_STAAM | Q99VG8 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:112
                                   239       249       259       269       279       289       299       309       319       329       339  
          METN2_STAAM   230 ENPQHTVTKRFVKEDLNDDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKMEVLRHG 341
               SCOP domains -----------------d3ceda1 A:247-341 Methionine import ATP-binding protein MetN2                                   SCOP domains
               CATH domains 3c              edA00 A:244-341  [code=3.30.70.260, no name defined]                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh--------------hhhhhhhhhhh.......eeeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3ced A 244 SN--------------ADDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKmEVLRHG 341
                             |       -      |249       259       269       279       289       299       309       319       329     | 339  
                             |            246                                                                                      335-MSE  
                           245                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with METN2_STAAM | Q99VG8 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:112
                                   239       249       259       269       279       289       299       309       319       329       339  
          METN2_STAAM   230 ENPQHTVTKRFVKEDLNDDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKMEVLRHG 341
               SCOP domains d3              cedb_ B: Methionine import ATP-binding protein MetN2                                             SCOP domains
               CATH domains 3c              edB00 B:244-341  [code=3.30.70.260, no name defined]                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh--------------hhhhhhhhhhh.......eeeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3ced B 244 SN--------------ADDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKmEVLRHG 341
                             |       -      |249       259       269       279       289       299       309       319       329     | 339  
                           245            246                                                                                      335-MSE  

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with METN2_STAAM | Q99VG8 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:112
                                   239       249       259       269       279       289       299       309       319       329       339  
          METN2_STAAM   230 ENPQHTVTKRFVKEDLNDDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKMEVLRHG 341
               SCOP domains d3              cedc_ C: Methionine import ATP-binding protein MetN2                                             SCOP domains
               CATH domains 3c              edC00 C:244-341  [code=3.30.70.260, no name defined]                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh--------------hhhhhhhhhh........eeeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3ced C 244 SN--------------ADDFETSLTELEPLEKDAYIVRLVFAGSTTTEPIVSSLSTAYDIKINILEANIKNTKNGTVGFLVLHIPYISSVDFGKFEKELIERQVKmEVLRHG 341
                             |       -      |249       259       269       279       289       299       309       319       329     | 339  
                           245            246                                                                                      335-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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CED)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (METN2_STAAM | Q99VG8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0015424    amino acid-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + amino acid(out/in) = ADP + phosphate + amino acid(in/out).
    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: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:0003333    amino acid transmembrane transport    The directed movement of amino acids, organic acids containing one or more amino substituents across a membrane by means of some agent such as a transporter or pore.
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015821    methionine transport    The directed movement of methionine, 2-amino-4-(methylthio)butanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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