1EK5 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+

Authors :   J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden

Date :   06 Mar 00 (Deposition) - 17 May 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Short-Chain Dehydrogenase, Epimerase, Galactosemia, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Crystallographic Evidence For Tyr 157 Functioning As The Active Site Base In Human Udp-Galactose 4-Epimerase.
Biochemistry V. 39 5691 2000
PubMed-ID: 10801319 | Reference-DOI: 10.1021/BI000215L
(for further references see the PDB file header)

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
	Chains	:	A
	EC Number	:	5.1.3.2
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Taxid	:	4932
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	FORESKIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:9 , GLY A:12 , TYR A:13 , ILE A:14 , ASP A:33 , ASN A:34 , PHE A:35 , HIS A:36 , ASN A:37 , ALA A:38 , MET A:65 , ASP A:66 , ILE A:67 , PHE A:88 , GLY A:90 , LYS A:92 , SER A:130 , SER A:131 , TYR A:157 , LYS A:161 , TYR A:185 , PHE A:186 , PRO A:188 , ASN A:206 , HOH A:605 , HOH A:606 , HOH A:625 , HOH A:631 , HOH A:653 , HOH A:655 , HOH A:656 , HOH A:658 , HOH A:660	BINDING SITE FOR RESIDUE NAD A 400

(no "SS Bond" information available for 1EK5)

Asymmetric Unit

No.	Residues
1	Leu A:142	-	Pro A:143

Asymmetric Unit (17, 17)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_037733	A	25	V	GALE_HUMAN	Disease (EDG)	---	A	A	25	V
02	UniProt	VAR_002539	N	34	S	GALE_HUMAN	Disease (EDG)	121908046	A	N	34	S
03	UniProt	VAR_037734	R	40	C	GALE_HUMAN	Disease (EDG)	144492228	A	R	40	C
04	UniProt	VAR_037735	D	69	E	GALE_HUMAN	Disease (EDG)	---	A	D	69	E
05	UniProt	VAR_002540	G	90	E	GALE_HUMAN	Disease (EDG)	28940882	A	G	90	E
06	UniProt	VAR_010058	V	94	M	GALE_HUMAN	Disease (EDG)	121908047	A	V	94	M
07	UniProt	VAR_002541	D	103	G	GALE_HUMAN	Disease (EDG)	28940883	A	D	103	G
08	UniProt	VAR_037736	E	165	K	GALE_HUMAN	Disease (EDG)	528467258	A	E	165	K
09	UniProt	VAR_037737	R	169	W	GALE_HUMAN	Disease (EDG)	137853859	A	R	169	W
10	UniProt	VAR_002542	A	180	V	GALE_HUMAN	Polymorphism	3204468	A	A	180	V
11	UniProt	VAR_002543	L	183	P	GALE_HUMAN	Disease (EDG)	121908045	A	L	183	P
12	UniProt	VAR_037738	R	239	W	GALE_HUMAN	Disease (EDG)	137853860	A	R	239	W
13	UniProt	VAR_002544	K	257	R	GALE_HUMAN	Disease (EDG)	28940884	A	K	257	R
14	UniProt	VAR_037739	G	302	D	GALE_HUMAN	Disease (EDG)	137853861	A	G	302	D
15	UniProt	VAR_002545	L	313	M	GALE_HUMAN	Disease (EDG)	3180383	A	L	313	M
16	UniProt	VAR_002546	G	319	E	GALE_HUMAN	Disease (EDG)	28940885	A	G	319	E
17	UniProt	VAR_037740	R	335	H	GALE_HUMAN	Disease (EDG)	368637540	A	R	335	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (17, 34)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_037733	A	25	V	GALE_HUMAN	Disease (EDG)	---	A	A	25	V
02	UniProt	VAR_002539	N	34	S	GALE_HUMAN	Disease (EDG)	121908046	A	N	34	S
03	UniProt	VAR_037734	R	40	C	GALE_HUMAN	Disease (EDG)	144492228	A	R	40	C
04	UniProt	VAR_037735	D	69	E	GALE_HUMAN	Disease (EDG)	---	A	D	69	E
05	UniProt	VAR_002540	G	90	E	GALE_HUMAN	Disease (EDG)	28940882	A	G	90	E
06	UniProt	VAR_010058	V	94	M	GALE_HUMAN	Disease (EDG)	121908047	A	V	94	M
07	UniProt	VAR_002541	D	103	G	GALE_HUMAN	Disease (EDG)	28940883	A	D	103	G
08	UniProt	VAR_037736	E	165	K	GALE_HUMAN	Disease (EDG)	528467258	A	E	165	K
09	UniProt	VAR_037737	R	169	W	GALE_HUMAN	Disease (EDG)	137853859	A	R	169	W
10	UniProt	VAR_002542	A	180	V	GALE_HUMAN	Polymorphism	3204468	A	A	180	V
11	UniProt	VAR_002543	L	183	P	GALE_HUMAN	Disease (EDG)	121908045	A	L	183	P
12	UniProt	VAR_037738	R	239	W	GALE_HUMAN	Disease (EDG)	137853860	A	R	239	W
13	UniProt	VAR_002544	K	257	R	GALE_HUMAN	Disease (EDG)	28940884	A	K	257	R
14	UniProt	VAR_037739	G	302	D	GALE_HUMAN	Disease (EDG)	137853861	A	G	302	D
15	UniProt	VAR_002545	L	313	M	GALE_HUMAN	Disease (EDG)	3180383	A	L	313	M
16	UniProt	VAR_002546	G	319	E	GALE_HUMAN	Disease (EDG)	28940885	A	G	319	E
17	UniProt	VAR_037740	R	335	H	GALE_HUMAN	Disease (EDG)	368637540	A	R	335	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1EK5)

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1j	ENST00000374497	1j	ENSE00001850298	chr1:24126892-24126877	16	GALE_HUMAN	-	0	0	-	-
1.1n	ENST00000374497	1n	ENSE00001372948	chr1:24125926-24125856	71	GALE_HUMAN	-	0	0	-	-
1.2b	ENST00000374497	2b	ENSE00002180266	chr1:24125502-24125377	126	GALE_HUMAN	1-41	41	1	A:1-41	41
1.2e	ENST00000374497	2e	ENSE00001691927	chr1:24125220-24125105	116	GALE_HUMAN	41-79	39	1	A:41-79	39
1.2h	ENST00000374497	2h	ENSE00000758318	chr1:24124720-24124607	114	GALE_HUMAN	80-117	38	1	A:80-117	38
1.3b	ENST00000374497	3b	ENSE00000758319	chr1:24124361-24124185	177	GALE_HUMAN	118-176	59	1	A:118-176	59
1.4d	ENST00000374497	4d	ENSE00000758320	chr1:24123637-24123524	114	GALE_HUMAN	177-214	38	1	A:177-214	38
1.5	ENST00000374497	5	ENSE00000758321	chr1:24123432-24123366	67	GALE_HUMAN	215-237	23	1	A:215-237	23
1.6a	ENST00000374497	6a	ENSE00000758322	chr1:24123272-24123187	86	GALE_HUMAN	237-265	29	1	A:237-265	29
1.6d	ENST00000374497	6d	ENSE00002163869	chr1:24123076-24122999	78	GALE_HUMAN	266-291	26	1	A:266-291	26
1.6e	ENST00000374497	6e	ENSE00002170745	chr1:24122755-24122641	115	GALE_HUMAN	292-330	39	1	A:292-330	39
1.6h	ENST00000374497	6h	ENSE00001893164	chr1:24122497-24122090	408	GALE_HUMAN	330-348	19	1	A:330-346	17

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:346
 aligned with GALE_HUMAN | Q14376 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
           GALE_HUMAN     1 MAEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
               SCOP domains d1ek5a_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1ek5A02 A:3-189,A:240-270 NAD(P)-binding Rossmann-like Domain                                                                                                                              1ek5A01 A:190-239,A:271-346                       1ek5A02 A:3-189,A:240-270      1ek5A01 A:190-239,A:271-346 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee............hhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeee..eee..................hhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhhh...eeeee......eehhhhhhhhhhhhh....eeee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------V--------S-----C----------------------------E--------------------E---M--------G-------------------------------------------------------------K---W----------V--P-------------------------------------------------------W-----------------R--------------------------------------------D----------M-----E---------------H----------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-41 UniProt: 1-41     --------------------------------------Exon 1.2h  PDB: A:80-117              Exon 1.3b  PDB: A:118-176 UniProt: 118-176                 Exon 1.4d  PDB: A:177-214             Exon 1.5  PDB: A:215-23----------------------------Exon 1.6d  PDB: A:266-291 Exon 1.6e  PDB: A:292-330              ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2e  PDB: A:41-79 UniProt: 41-79 -------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:237-265    ----------------------------------------------------------------Exon 1.6h         Transcript 1 (2)
                 1ek5 A   1 MAEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

1ek5A02

A:3-189,A:240-270

Architecture: Alpha-Beta Complex (3881)

Topology: UDP-galactose 4-epimerase; domain 1 (99)

Homologous Superfamily: UDP-galactose 4-epimerase, domain 1 (99)

Human (Homo sapiens) (8)

1ek5A01

A:190-239,A:271-346

(no "Pfam Domain" information available for 1EK5)

Asymmetric Unit(hide GO term definitions)

Chain A (GALE_HUMAN | Q14376)

molecular function
	GO:0003974	UDP-N-acetylglucosamine 4-epimerase activity	Catalysis of the reaction: UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-galactosamine.
	GO:0003978	UDP-glucose 4-epimerase activity	Catalysis of the reaction: UDP-glucose = UDP-galactose.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016857	racemase and epimerase activity, acting on carbohydrates and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019388	galactose catabolic process	The chemical reactions and pathways resulting in the breakdown of galactose, the aldohexose galacto-hexose.
	GO:0006012	galactose metabolic process	The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

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	GALE_HUMAN \| Q14376	:	1ek6 1hzj 1i3k 1i3l 1i3m 1i3n

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