3K3G - JenaLib

Title :   CRYSTAL STRUCTURE OF THE UREA TRANSPORTER FROM DESULFOVIBRIO VULGARIS BOUND TO 1,3-DIMETHYLUREA

Authors :   E. J. Levin, M. Zhou, New York Consortium On Membrane Protein Str (Nycomps)

Date :   02 Oct 09 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Membrane Protein, Channel, Urea Transport, Transporter, Transport Protein, Structural Genomics, Psi-2, Protein Structure Initiative, New York Consortium On Membrane Protein Structure, Nycomps (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Levin, M. Quick, M. Zhou
Crystal Structure Of A Bacterial Homologue Of The Kidney Urea Transporter.
Nature V. 462 757 2009
PubMed-ID: 19865084 | Reference-DOI: 10.1038/NATURE08558

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:24	BINDING SITE FOR RESIDUE AU A 338
02	AC2	SOFTWARE	CYS A:19 , THR A:31 , LEU A:35 , AU A:340 , AU A:341	BINDING SITE FOR RESIDUE AU A 339
03	AC3	SOFTWARE	CYS A:15 , CYS A:19 , AU A:339 , AU A:341 , AU A:342	BINDING SITE FOR RESIDUE AU A 340
04	AC4	SOFTWARE	CYS A:15 , ASP A:16 , AU A:339 , AU A:340 , AU A:342	BINDING SITE FOR RESIDUE AU A 341
05	AC5	SOFTWARE	CYS A:15 , AU A:340 , AU A:341	BINDING SITE FOR RESIDUE AU A 342
06	AC6	SOFTWARE	THR A:47 , VAL A:50 , CYS A:51 , AU A:344	BINDING SITE FOR RESIDUE AU A 343
07	AC7	SOFTWARE	THR A:47 , CYS A:51 , AU A:343	BINDING SITE FOR RESIDUE AU A 344
08	AC8	SOFTWARE	CYS A:224 , AU A:346	BINDING SITE FOR RESIDUE AU A 345
09	AC9	SOFTWARE	CYS A:224 , AU A:345	BINDING SITE FOR RESIDUE AU A 346
10	BC1	SOFTWARE	GLU A:187 , VAL A:188 , PHE A:190 , PHE A:243 , HOH A:359	BINDING SITE FOR RESIDUE MMU A 347
11	BC2	SOFTWARE	GLN A:24 , VAL A:25 , PHE A:27 , LEU A:77 , PHE A:80 , LEU A:129 , THR A:130 , HOH A:370	BINDING SITE FOR RESIDUE MMU A 348

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:331
 aligned with UT_DESVH | Q72CX3 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                             1                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
             UT_DESVH     - -MFGEQLLKNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSVAGLADMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k3gA00 A:0-334 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................----.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3g A   0 RAFGEQLLKNPLIEFCDSVCRGCGQVMFQNNTVTGLLFFAGIFYNSTTLGVCAVLGTAASTLTAQLLGVDKPLVRAGLFGFNGTLAGIALPFFFNYEPAMLGYVALNGAFTTIIMASLLNFLGKWGVPALTAPFVLATWLLMFGVYKLSLFHPGALIAPALPSV----DMGTVTGRTFMEGLFKGVGEVMFQDNIVTGVIFVVAILVNSRISALFAVIGSLVGLCTALIMHSPETPVRLGLYGFNSVLCGIAMGGIFFYLNIRTFLYALGCMVLGAIATGAFSVLLSPIGMPALTWPFIVVTWLFLFAGSMFRNIAQVPTEKAGTPEDNLRSLAI 334
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   |   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
                                                                                                                                                                                             163  168

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 (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (UT_DESVH | Q72CX3)

molecular function
	GO:0033219	urea binding	Interacting selectively and non-covalently with urea, a water-soluble carboxamide with the structure H2N-CO-NH2.
	GO:0015265	urea channel activity	Enables the facilitated diffusion of urea (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0015204	urea transmembrane transporter activity	Enables the directed movement of urea cross a membrane into, out of or within a cell, or between cells. Urea is the water soluble compound H2N-CO-NH2.
biological process
	GO:0070207	protein homotrimerization	The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
	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.
	GO:0071918	urea transmembrane transport	The process in which urea, the water-soluble compound H2N-CO-NH2, is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
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:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in 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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