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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A CBS DOMAIN FROM A PUTATIVE METAL ION TRANSPORTER BOUND TO AMP FROM PSEUDOMONAS SYRINGAE TO 1.55A
 
Authors :  A. J. Stein, L. Bigelow, G. Cobb, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  18 Jan 10  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metal-Ion, Cbs, Amp, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, L. Bigelow, G. Cobb, A. Joachimiak
The Crystal Structure Of A Cbs Domain From A Putative Metal Ion Transporter Bound To Amp From Pseudomonas Syringae To 1. 55A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE METAL ION TRANSPORTER
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 59-194
    Gene: PSPTO4807, PSPTO_4807
    Organism Scientific: PSEUDOMONAS SYRINGAE
    Organism Taxid: 223283
    Strain: PV. TOMATO STR. DC3000

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:4 , VAL A:68 , GLN A:72 , ILE A:74 , HIS A:94 , SER A:95 , ARG A:96 , PRO A:98 , MSE A:160 , THR A:175 , ASP A:178 , HOH A:197 , HOH A:240 , HOH A:241 , HOH A:243BINDING SITE FOR RESIDUE AMP A 1
2AC2SOFTWARELYS A:114 , HOH B:1 , HOH B:13 , VAL B:68 , GLN B:72 , ILE B:74 , HIS B:94 , SER B:95 , ARG B:96 , MSE B:160 , THR B:175 , GLU B:177 , ASP B:178 , HOH B:206 , HOH B:229BINDING SITE FOR RESIDUE AMP B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LFR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LFR)

(-) 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:123
 aligned with Q87VX8_PSESM | Q87VX8 from UniProtKB/TrEMBL  Length:280

    Alignment length:123
                                    70        80        90       100       110       120       130       140       150       160       170       180   
         Q87VX8_PSESM    61 LQVRDIMVPRSQMISIKATQTPREFLPAVIDAAHSRYPVIGESHDDVLGVLLAKDLLPLILKADGDSDDVKKLLRPATFVPESKRLNVLLREFRANHNHMAIVIDEYGGVAGLVTIEDVLEQI 183
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhee.hhh..ee...hhhhhhhhhhhhh..eeeee......eeeeee.hhhhhhhhh.hhhhhhhhhh.....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfr A  61 LQVRDImVPRSQmISIKATQTPREFLPAVIDAAHSRYPVIGESHDDVLGVLLAKDLLPLILKADGDSDDVKKLLRPATFVPESKRLNVLLREFRANHNHmAIVIDEYGGVAGLVTIEDVLEQI 183
                                  | 70  |     80        90       100       110       120       130       140       150       160       170       180   
                                 67-MSE |                                                                                    160-MSE                   
                                       73-MSE                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with Q87VX8_PSESM | Q87VX8 from UniProtKB/TrEMBL  Length:280

    Alignment length:130
                                    68        78        88        98       108       118       128       138       148       158       168       178       188
         Q87VX8_PSESM    59 ADLQVRDIMVPRSQMISIKATQTPREFLPAVIDAAHSRYPVIGESHDDVLGVLLAKDLLPLILKADGDSDDVKKLLRPATFVPESKRLNVLLREFRANHNHMAIVIDEYGGVAGLVTIEDVLEQIVGDIE 188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------CBS-3lfrB01 B:130-185                                   --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------CBS-3lfrB02 B:130-185                                   --- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------CBS-3lfrB03 B:130-185                                   --- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------CBS-3lfrB04 B:130-185                                   --- Pfam domains (4)
         Sec.struct. author ...hhhhh.ee.hhh..ee...hhhhhhhhhhhhh..eeeee......eeeeee.hhhhhhhh..-...-hhhhhh....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfr B  59 ADLQVRDImVPRSQmISIKATQTPREFLPAVIDAAHSRYPVIGESHDDVLGVLLAKDLLPLILKA-GDS-DVKKLLRPATFVPESKRLNVLLREFRANHNHmAIVIDEYGGVAGLVTIEDVLEQIVGDIE 188
                                    68    |   78        88        98       108       118    | | |-|      138       148       158 |     168       178       188
                                   67-MSE |                                               123 | | |                            160-MSE                        
                                         73-MSE                                             125 | |                                                           
                                                                                              127 |                                                           
                                                                                                129
   Legend:   → Mismatch (orange background)
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  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 3LFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CBS] (51)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87VX8_PSESM | Q87VX8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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