2B69 - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN UDP-GLUCORONIC ACID DECARBOXYLASE

Authors :   E. Ugochukwu, E. Dubinina, K. Kavanagh, M. Sundstrom, J. Weigelt, A. Ed C. Arrowsmith, F. Von Delft, U. Oppermann, Structural Genomics Co (Sgc)

Date :   30 Sep 05 (Deposition) - 18 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.21

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Udp-Glucoronic Acid Decarboxylase, Structural Genomics, Structural Genomics Consortium, Sgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, E. Dubinina, K. Kavanagh, M. Sundstrom, J. Weigelt, A. Edwards, C. Arrowsmith, F. Von Delft, U. Oppermann
Crystal Structure Of Human Udp-Glucoronic Acid Decarboxylas
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:11 , ALA A:13 , GLY A:14 , PHE A:15 , VAL A:16 , ASP A:35 , ASN A:36 , PHE A:37 , PHE A:38 , THR A:39 , GLY A:40 , HIS A:59 , ASP A:60 , VAL A:61 , LEU A:75 , ALA A:76 , SER A:77 , ALA A:79 , THR A:94 , SER A:117 , THR A:118 , TYR A:147 , LYS A:151 , ILE A:174 , ASN A:176 , THR A:177 , ARG A:188 , HOH A:905 , HOH A:922 , HOH A:925 , HOH A:969 , HOH A:999	BINDING SITE FOR RESIDUE NAD A 800
2	AC2	SOFTWARE	PRO A:81 , ARG A:144 , ASN A:176 , ARG A:188 , VAL A:189 , ASN A:192 , THR A:204 , VAL A:205 , TYR A:206 , GLN A:211 , ARG A:213 , ILE A:247 , ASP A:273 , ARG A:277 , HOH A:934 , HOH A:940 , HOH A:942 , HOH A:980 , HOH A:1029	BINDING SITE FOR RESIDUE UDP A 900
3	AC3	SOFTWARE	PRO A:64 , LEU A:65 , TYR A:66 , LEU A:100 , ASN A:101 , GLY A:104 , LEU A:105 , LYS A:107 , ARG A:108 , TYR A:161 , HOH A:918 , HOH A:929 , HOH A:981 , HOH A:985 , HOH A:1183	BINDING SITE FOR RESIDUE UDP A 901

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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:312
 aligned with UXS1_HUMAN | Q8NBZ7 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:312
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397  
           UXS1_HUMAN    88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPPNYMYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLSEAQDDPQKRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQA 399
               SCOP domains d2b69a1 A:4-315 UDP-glucuronate decarboxylase 1                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh....................hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.........hhhhhhhhhhhhh..eeee.....eee.eehhhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b69 A   4 RKRILITGGAGFVGSHLTDKLmmDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPPNYmYNPIKTLKTNTIGTLNmLGLAKRVGARLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETmCYAYmKQEGVEVRVARIFNTFGPRmHmNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALmNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLSEAQDDPQKRKPDIKKAKLmLGWEPVVPLEEGLNKAIHYFRKELEYQA 315
                                    13        23 ||     33        43        53        63        73        83 |      93       103       113       123       133       143       153   |   163       173       183|      193       203       213       223     | 233       243       253       263       273       283   |   293       303       313  
                                                25-MSE                                                      85-MSE          102-MSE                                                157-MSE|                 182-MSE                                        229-MSE                                                   287-MSE                        
                                                 26-MSE                                                                                                                                 162-MSE               184-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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A (UXS1_HUMAN | Q8NBZ7)

molecular function
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0048040	UDP-glucuronate decarboxylase activity	Catalysis of the reaction: H(+) + UDP-alpha-D-glucuronate = CO(2) + UDP-alpha-D-xylose.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0033320	UDP-D-xylose biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-D-xylose, uridinediphosphoxylose, a substance composed of xylose in glycosidic linkage with uridine diphosphate.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0032580	Golgi cisterna membrane	The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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