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(-) Description

Title :  CRYSTAL STRUCTURE OF TRKA-N DOMAIN OF INNER MEMBRANE PROTEIN YBAL FROM ESCHERICHIA COLI
 
Authors :  C. Chang, L. Bigelow, K. Buck, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  19 Jan 09  (Deposition) - 10 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trka-N Domain, Ybal, E. Coli, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Antiport, Cell Inner Membrane, Cell Membrane, Ion Transport, Membrane, Transmembrane, Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, L. Bigelow, K. Buck, A. Joachimiak
Crystal Structure Of Trka-N Domain Of Inner Membrane Protei Ybal From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INNER MEMBRANE PROTEIN YBAL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DOMAIN TRKA-N, RESIDUES 414-550
    Gene: B0478, ESCHERICHIA COLI CFT073, JW0467, YBAL, YLAA
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:4 , HOH A:36 , HOH A:79 , HOH A:106 , HOH A:120 , GLY A:424 , GLY A:426 , ARG A:427 , VAL A:428 , GLU A:447 , THR A:448 , ARG A:452 , GLY A:466 , ASN A:467 , ALA A:468 , ILE A:489 , GLU A:494 , ARG A:514BINDING SITE FOR RESIDUE AMP A 601
2AC2SOFTWAREHOH B:8 , HOH B:39 , HOH B:176 , HOH B:180 , GLY B:424 , GLY B:426 , ARG B:427 , VAL B:428 , GLU B:447 , THR B:448 , GLY B:466 , ASN B:467 , ALA B:468 , ILE B:489 , GLU B:494 , ARG B:514BINDING SITE FOR RESIDUE AMP B 601
3AC3SOFTWAREHOH A:54 , HOH B:17 , HOH B:18 , HOH B:59 , HOH B:82BINDING SITE FOR RESIDUE MG B 602

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:417 -A:481
2B:417 -B:481

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RCK_NPS51201 RCK N-terminal domain profile.YBAL_ECOLI419-541
 		  2A:419-541
B:419-541

(-) Exons   (0, 0)

(no "Exon" information available for 3FWZ)

(-) 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    
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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:140
 aligned with YBAL_ECOLI | P39830 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:140
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550
           YBAL_ECOLI   411 QIPVDICNHALLVGYGRVGSLLGEKLLASDIPLVVIETSRTRVDELRERGVRAVLGNAANEEIMQLAHLECAKWLILTIPNGYEAGEIVASARAKNPDIEIIARAHYDDEVAYITERGANQVVMGEREIARTMLELLETP 550
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fwzA00 A:411-550 NAD(P)-binding Rossmann-like Domain                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh..eeee....hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------RCK_N  PDB: A:419-541 UniProt: 419-541                                                                                     --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwz A 411 SNAVDICNHALLVGYGRVGSLLGEKLLASDIPLVVIETSRTRVDELRERGVRAVLGNAANEEImQLAHLECAKWLILTIPNGYEAGEIVASARAKNPDIEIIARAHYDDEVAYITERGANQVVmGEREIARTmLELLETP 550
                                   420       430       440       450       460       470   |   480       490       500       510       520       530   |   540  |    550
                                                                                         474-MSE                                                     534-MSE  543-MSE   


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with YBAL_ECOLI | P39830 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:135
                                   423       433       443       453       463       473       483       493       503       513       523       533       543     
           YBAL_ECOLI   414 VDICNHALLVGYGRVGSLLGEKLLASDIPLVVIETSRTRVDELRERGVRAVLGNAANEEIMQLAHLECAKWLILTIPNGYEAGEIVASARAKNPDIEIIARAHYDDEVAYITERGANQVVMGEREIARTMLELLE 548
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fwzB00 B:414-548 NAD(P)-binding Rossmann-like Domain                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh..eeee....hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RCK_N  PDB: B:419-541 UniProt: 419-541                                                                                     ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwz B 414 VDICNHALLVGYGRVGSLLGEKLLASDIPLVVIETSRTRVDELRERGVRAVLGNAANEEImQLAHLECAKWLILTIPNGYEAGEIVASARAKNPDIEIIARAHYDDEVAYITERGANQVVmGEREIARTmLELLE 548
                                   423       433       443       453       463       473|      483       493       503       513       523       533|      543     
                                                                                      474-MSE                                                     534-MSE  543-MSE
   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 3FWZ)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YBAL_ECOLI | P39830)
molecular function
    GO:0015297    antiporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
    GO:0008324    cation transmembrane transporter activity    Enables the transfer of cation from one side of the membrane to the other.
    GO:0015299    solute:proton antiporter activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + H+(in) = solute(in) + H+(out).
biological process
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) 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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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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  3fwz
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  YBAL_ECOLI | P39830
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