4J7H - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF EVAA, A 2,3-DEHYDRATASE IN COMPLEX WITH DTDP-BENZENE AND DTDP-RHAMNOSE

Authors :   H. M. Holden, R. L. Kubiak, J. B. Thoden

Date :   13 Feb 13 (Deposition) - 22 May 13 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.69

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (2x)
Biol. Unit 2: B  (2x)
Biol. Unit 3: A (2x),B (2x)

Keywords :   Nudix Hydrolase Superfamily, Dehydration, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Kubiak, J. B. Thoden, H. M. Holden
Structure Of Evaa: A Paradigm For Sugar 2, 3-Dehydratases.
Biochemistry V. 52 2078 2013
PubMed-ID: 23473392 | Reference-DOI: 10.1021/BI400176N

Molecule 1 - EVAA 2,3-DEHYDRATASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28JT
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	EVAA
	Mutation	:	YES
	Organism Scientific	:	AMYCOLATOPSIS ORIENTALIS
	Organism Taxid	:	31958
	Strain	:	NRRL 18098
	Synonym	:	PCZA361.3

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B
Biological Unit 3 (2x)	:	A (2x)	B (2x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	TLO	2	Ligand/Ion	5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE
3	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	TLO	2	Ligand/Ion	5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE
3	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	TLO	2	Ligand/Ion	5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE
3	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Biological Unit 3 (3, 12)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	TLO	2	Ligand/Ion	5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE
3	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:67 , PHE A:83 , GLN A:153 , ALA A:154 , ASN A:158 , ASN A:200 , TRP A:320 , THR A:321 , GLN A:322 , ARG A:408 , HOH A:734 , HOH A:813 , HOH A:814 , HOH A:903 , HOH A:977	BINDING SITE FOR RESIDUE TLO A 501
2	AC2	SOFTWARE	ARG A:104 , TRP A:106 , GLN A:107 , GLN A:108 , SER A:193 , TRP A:194 , TRP A:288 , TYR A:302 , VAL A:333 , ARG A:351 , GLN A:367 , CYS A:368 , THR A:369 , ASN A:372 , TYR A:373 , HOH A:617 , HOH A:618 , HOH A:698 , HOH A:704 , HOH A:719 , HOH A:750 , HOH A:751 , HOH A:949	BINDING SITE FOR RESIDUE TRH A 502
3	AC3	SOFTWARE	ARG A:112 , ARG A:276 , ARG A:279 , HOH A:835	BINDING SITE FOR RESIDUE EDO A 503
4	AC4	SOFTWARE	ALA A:391 , ARG A:393 , ARG A:415 , TRP B:214 , ASP B:215 , HOH B:794	BINDING SITE FOR RESIDUE EDO A 504
5	AC5	SOFTWARE	PRO A:392 , ARG A:395 , ILE A:419 , ASP A:420 , ASP A:422 , HOH A:761	BINDING SITE FOR RESIDUE EDO A 505
6	AC6	SOFTWARE	TRP B:67 , PHE B:83 , GLN B:153 , ALA B:154 , THR B:155 , ASN B:158 , ASN B:200 , TRP B:320 , THR B:321 , GLN B:322 , ARG B:408 , HOH B:803 , HOH B:804 , HOH B:811 , HOH B:911	BINDING SITE FOR RESIDUE TLO B 501
7	AC7	SOFTWARE	ARG B:104 , TRP B:106 , GLN B:107 , GLN B:108 , SER B:193 , TRP B:194 , TRP B:288 , TYR B:302 , VAL B:333 , ARG B:351 , GLN B:367 , CYS B:368 , THR B:369 , ASN B:372 , TYR B:373 , HOH B:642 , HOH B:742 , HOH B:747 , HOH B:818 , HOH B:819 , HOH B:820 , HOH B:821 , HOH B:946	BINDING SITE FOR RESIDUE TRH B 502
8	AC8	SOFTWARE	ARG B:112 , ARG B:276 , ARG B:279 , HOH B:901	BINDING SITE FOR RESIDUE EDO B 503
9	AC9	SOFTWARE	LEU B:387 , ARG B:395 , ASP B:420 , ASP B:422 , ILE B:425	BINDING SITE FOR RESIDUE EDO B 504

Asymmetric Unit

No.	Residues
1	A:286	-	B:286

Asymmetric Unit

No.	Residues
1	Gly A:101	-	Pro A:102
2	Ala A:175	-	Pro A:176
3	Gly B:101	-	Pro B:102
4	Ala B:175	-	Pro B:176

(no "SAP(SNP)/Variant" information available for 4J7H)

(no "PROSITE Motif" information available for 4J7H)

(no "Exon" information available for 4J7H)

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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeehhhhh..eee......eee......eeeeeeeeee.........eeeeeeeee....eeeeeeeeee..eeeeeeeeee.......eeee..eeehhhhh...hhhhh...hhh.eeeeeeee.........eeeeeeee..........eeeeehhhhhhhhh.....hhhhhhhhhh............hhhhhhhhhhhhhhh.eeeeeeehhhhh..eee....eee.....eeeeeeeee...eeeeeeee...eeeeeeeeee..eeeeeeeeee.......eeee..eeehhhhhh..hhhhh..hhhhhhh.hhh.eeeeeeee.........eeeeeeee..........eeeehhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7h A  11 AVRPRDHHDYADRIALSAATTDGVQMRTEDVRAWIAERRDANVFHVERIPFADLDQWWFEGVTGNLVHRSGRFFTIEGLHVIEHDGPHGDGPYREWQQPVIRQPEVGILGILAKEFDGVLHFLMQAKMEPGNPNLVQLSPTVQATRSNYNVKLIEYFAPPDPERVIVDVLQAEQGSWFFRKSNRNMIVETVDDVPLWDDFCWLTLGQIAELMHEDETINMNSRSVLSCLPYQDITPRALFSDVQLLSWFTNERSRHDVRVRRIPLADVCGWKQGAEEIEHEDGRYFKVLAVAVKKISWTQPLVESVDLGVVAFLVRKIDGVPHVLVQARVDGGFLDTVELAPTVQCTPLNYAHLPAEEAPPFLDLVQNAPRSRIRYEAIHSEEGGRFLGVRARYLVIDADEAIDPPPGYAWVTPAQLTALTRHGHYVNVEARTLLACINAAAAQPR 468
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   ||  322       332       342       352       362       372       382       392       402       412       422       432       442       452       462      
                                                                                                                                                                              159|                                                                                                                                             311|                                                                                                                                                       
                                                                                                                                                                               167                                                                                                                                              317

Chain B from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeehhhhh..eee......eee......eeeeeeeeee.........eeeeeeeee.....eeeeeeeee..eeeeeeeeee.......eeee..eee.......hhhhhh..hhh.eeeeeeee.........eeeeeeee..........eeeeehhhhhhhh......hhhhhhhhh.............hhhhhhhhhhhhhhh.eeeeeeehhhhh..eee....eee.....eeeeeeeee..eeeeeeee...eeeeeeeeee..eeeeeeeeee.......eeee..eeehhhhhh..hhhhh..hhhhhhh.hhh.eeeeeeee.........eeeeeeee..........eeeehhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j7h B  11 AVRPRDHHDYADRIALSAATTDGVQMRTEDVRAWIAERRDANVFHVERIPFADLDQWWFEGVTGNLVHRSGRFFTIEGLHVIEHDGPHGDGPYREWQQPVIRQPEVGILGILAKEFDGVLHFLMQAKMEPGNPNLVQLSPTVQATRSNNVKLIEYFAPPDPERVIVDVLQAEQGSWFFRKSNRNMIVETVDDVPLWDDFCWLTLGQIAELMHEDETINMNSRSVLSCLPYQDITPRALFSDVQLLSWFTNERSRHDVRVRRIPLADVCGWKQGAEEIEHEDGRYFKVLAVAVKGSWTQPLVESVDLGVVAFLVRKIDGVPHVLVQARVDGGFLDTVELAPTVQCTPLNYAHLPAEEAPPFLDLVQNAPRSRIRYEAIHSEEGGRFLGVRARYLVIDADEAIDPPPGYAWVTPAQLTALTRHGHYVNVEARTLLACINAAAAQPR 468
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   ||  324       334       344       354       364       374       384       394       404       414       424       434       444       454       464    
                                                                                                                                                                             158|                                                                                                                                              312|                                                                                                                                                     
                                                                                                                                                                              167                                                                                                                                               319

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 '\|'

(no "SCOP Domain" information available for 4J7H)

(no "CATH Domain" information available for 4J7H)

(no "Pfam Domain" information available for 4J7H)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4J7H)

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 ]
		TLO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRH	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:175 - Pro A:176	[ RasMol ]
		Ala B:175 - Pro B:176	[ RasMol ]
		Gly A:101 - Pro A:102	[ RasMol ]
		Gly B:101 - Pro B:102	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	4j7h
		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
	O52793_AMYOR \| O52793
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		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
	O52793_AMYOR \| O52793
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O52793_AMYOR \| O52793	:	4j7g

4j7g	CRYSTAL STRUCTURE OF EVAA, A 2,3-DEHYDRATASE IN COMPLEX WITH DTDP-FUCOSE AND DTDP-RHAMNOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (9, 9)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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