1NAH - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, REDUCED

Authors :   J. B. Thoden, P. A. Frey, H. M. Holden

Date :   22 Nov 95 (Deposition) - 23 Dec 96 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Thoden, P. A. Frey, H. M. Holden
Crystal Structures Of The Oxidized And Reduced Forms Of Udp-Galactose 4-Epimerase Isolated From Escherichia Coli.
Biochemistry V. 35 2557 1996
PubMed-ID: 8611559 | Reference-DOI: 10.1021/BI952715Y

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
	Chains	:	A
	EC Number	:	5.1.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7E2
	Expression System Strain	:	BL21(DE3), PLYSS
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	REDUCED FORM
	Synonym	:	EPIMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	NA	2	Ligand/Ion	SODIUM ION
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:334 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:552	BINDING SITE FOR RESIDUE NA A 339
2	AC2	SOFTWARE	GLN A:91 , HOH A:516 , HOH A:526 , HOH A:527 , HOH A:528 , HOH A:687	BINDING SITE FOR RESIDUE NA A 340
3	AC3	SOFTWARE	GLY A:7 , GLY A:10 , TYR A:11 , ILE A:12 , ASP A:31 , ASN A:32 , LEU A:33 , CYS A:34 , ASN A:35 , SER A:36 , GLY A:57 , ASP A:58 , ILE A:59 , PHE A:80 , ALA A:81 , GLY A:82 , LYS A:84 , ASN A:99 , SER A:122 , SER A:124 , TYR A:149 , LYS A:153 , TYR A:177 , PHE A:178 , PRO A:180 , EDO A:343 , HOH A:359 , HOH A:360 , HOH A:392 , HOH A:447 , HOH A:448 , HOH A:679	BINDING SITE FOR RESIDUE NAD A 341
4	AC4	SOFTWARE	ASN A:179 , ASN A:198 , ASN A:199 , LEU A:200 , ALA A:216 , ILE A:217 , PHE A:218 , ARG A:231 , TYR A:233 , ARG A:292 , ASP A:295 , TYR A:299 , HOH A:477 , HOH A:532 , HOH A:557 , HOH A:561 , HOH A:564 , HOH A:581 , HOH A:640 , HOH A:693 , HOH A:713 , HOH A:768	BINDING SITE FOR RESIDUE UDP A 342
5	AC5	SOFTWARE	TYR A:11 , ASN A:35 , ASP A:192 , NAD A:341 , HOH A:363 , HOH A:545	BINDING SITE FOR RESIDUE EDO A 343
6	AC6	SOFTWARE	LEU A:250 , LYS A:253 , TYR A:259 , GLU A:309	BINDING SITE FOR RESIDUE PEG A 344

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

Asymmetric Unit

No.	Residues
1	Ile A:134	-	Pro A:135

(no "SAP(SNP)/Variant" information available for 1NAH)

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

(no "Exon" information available for 1NAH)

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:338
 aligned with GALE_ECOLI | P09147 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    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        
           GALE_ECOLI     1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
               SCOP domains d1naha_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1nahA02 A:1-181,A:232-262 NAD(P)-binding Rossmann-like Domain                                                                                                                        1nahA01 A:182-231,A:263-338                       1nahA02 A:1-181,A:232-262      1nahA01 A:182-231,A:263-338 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains --Epimerase-1nahA01 A:3-262                                                                                                                                                                                                                                           ------------Epimerase_Csub-1nahA02 A:275-336                              -- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhh.....eeeeee......hhhhhhhh.......eeee.....hhhhhhhh......eeee......hhhhhh.hhhhhhhhhhhhhhhhhhh......eeeeeee.......................hhhhhhhhhhhhhhhhhhh....eeeeeee.eee..................hhhhhhh........eeee..............eeehhhhhhhhhhhhhh.....eeeeeee.......hhhhhhhhh........eeee..............hhhhhh........hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nah A   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDNPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
                                    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

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)

Escherichia coli. Organism_taxid: 562. (49)

1nahA02

A:1-181,A:232-262

Architecture: Alpha-Beta Complex (3881)

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

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

Escherichia coli. Organism_taxid: 562. (15)

1nahA01

A:182-231,A:263-338

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Epimerase (42)

Escherichia coli (strain K12) (19)

Epimerase-1nahA01

A:3-262

Clan: no clan defined [family: Epimerase_Csub] (12)

Family: Epimerase_Csub (12)

Escherichia coli (strain K12) (12)

Epimerase_Csub-1nahA02

A:275-336

Asymmetric Unit(hide GO term definitions)

Chain A (GALE_ECOLI | P09147)

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:0003978	UDP-glucose 4-epimerase activity	Catalysis of the reaction: UDP-glucose = UDP-galactose.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0009242	colanic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of colanic acid, a capsular bacterial polysaccharide.
	GO:0033499	galactose catabolic process via UDP-galactose	The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:134 - Pro A:135	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nah
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GALE_ECOLI \| P09147
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.1.3.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GALE_ECOLI \| P09147
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1NAH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

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

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File