4F97 - JenaLib

Title :   CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX WITH GDP AND VALIDOXYLAMINE A 7'-PHOSPHATE

Authors :   M. C. Cavalier, Y. -S. Yim, S. Asamizu, D. Neau, K. H. Almabruk, T. Mahmud

Date :   18 May 12 (Deposition) - 17 Oct 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

Chains :   Asym./Biol. Unit : A,B

Keywords :   Twin Rossman Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Cavalier, Y. S. Yim, S. Asamizu, D. Neau, K. H. Almabruk, T. Mahmud Y. H. Lee
Mechanistic Insights Into Validoxylamine A 7'-Phosphate Synthesis By Vlde Using The Structure Of The Entire Product Complex.
Plos One V. 7 44934 2012
PubMed-ID: 23028689 | Reference-DOI: 10.1371/JOURNAL.PONE.0044934

Compounds

Molecule 1 - VLDE
	Chains	:	A, B
	EC Number	:	2.4.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	VLDE
	Organism Scientific	:	STREPTOMYCES HYGROSCOPICUS SUBSP. LIMONEUS
	Organism Taxid	:	264445
	Synonym	:	PSEUDO-GLYCOSYLTRANSFERASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	VDO	2	Ligand/Ion	[(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:290 , LYS A:295 , ARG A:321 , ASN A:323 , ASP A:360 , ASN A:361 , ASP A:362 , VAL A:363 , THR A:366 , ASN A:386 , LEU A:387 , SER A:388 , GLU A:391 , VDO A:502 , HOH A:645 , HOH A:674 , HOH A:676 , HOH A:683 , HOH A:689 , HOH A:706	BINDING SITE FOR RESIDUE GDP A 501
2	AC2	SOFTWARE	ASP A:158 , HIS A:182 , ILE A:183 , ARG A:290 , ASN A:325 , ARG A:326 , ASP A:383 , GLY A:384 , GLN A:385 , ASN A:386 , GDP A:501 , HOH A:804	BINDING SITE FOR RESIDUE VDO A 502
3	AC3	SOFTWARE	ARG A:218 , TRP A:219 , GLU A:406 , THR A:407 , CYS A:408 , GLU A:412 , HOH A:714	BINDING SITE FOR RESIDUE EDO A 503
4	AC4	SOFTWARE	TYR A:110 , SER A:187 , ARG B:114 , CL B:504	BINDING SITE FOR RESIDUE CL A 504
5	AC5	SOFTWARE	ASP B:158 , HIS B:182 , ILE B:183 , PHE B:215 , ARG B:290 , ASN B:325 , ARG B:326 , ASP B:383 , GLY B:384 , GLN B:385 , ASN B:386 , GDP B:502 , HOH B:740 , HOH B:770	BINDING SITE FOR RESIDUE VDO B 501
6	AC6	SOFTWARE	ARG B:290 , LYS B:295 , ARG B:321 , ASN B:323 , ASP B:360 , ASN B:361 , ASP B:362 , VAL B:363 , THR B:366 , ASN B:386 , LEU B:387 , SER B:388 , GLU B:391 , VDO B:501 , HOH B:659 , HOH B:667 , HOH B:684 , HOH B:692 , HOH B:693	BINDING SITE FOR RESIDUE GDP B 502
7	AC7	SOFTWARE	ARG B:218 , TRP B:219 , GLU B:406 , THR B:407 , CYS B:408 , GLU B:412 , HOH B:617 , HOH B:672	BINDING SITE FOR RESIDUE EDO B 503
8	AC8	SOFTWARE	ARG A:114 , CL A:504 , TYR B:110 , SER B:187	BINDING SITE FOR RESIDUE CL B 504

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeee......eeeee...hhhhhhhh...eeeeeeeee..hhhhhhhhhhh...eeeeehhheeeeeeee..hhhhhhhhhhhhh..hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhh....eeee......hhhhhh..hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eee....eeee..eeeeeee..............hhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh....eeeee....hhhhhhhhheee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f97 A   3 GSEIFLASKRAAITYDTDPATGEPRAWLAPGGTGNVVAEQAGVLNISWIASADSEDDRRASALNPDGVTMELHSGREILVRLIRHDPAVFRNVQNFMTANLMWAANNYGWDRWTQPSFGSDAREGWADFGRFTRDFADAILKSSAQSADPVYLVHDYQLVGVPALLREQRPDAPILLFVHIPWPSADYWRILPKEIRTGILHGMLPATTIGFFADRWCRNFLESVADLLPDARIDREAMTVEWRGHRTRLRTMPLGYSPLTPQLPEGIEEWADGHRLVVHSGRTDPIKNAERAVRAFVLAARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGSDTVRIDNDNDVNHTIACFRRADLLIFNSTVDGQNLSTFEAPLVNERDADVILSETCGAAEVLGEYCRSVNPFDLVEQAEAISAALAAGPRQRAEAAARRRDAARPWTLEAWVQAQLDGLAADHAART 479
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262||     277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477  
                                                                                                                                                                                                                                                                                              263|                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                               269

Chain B from PDB  Type:PROTEIN  Length:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeee......eeeee...hhhhhhhhh..eeeeeeeee..hhhhhhhhhhh...eee....eeeeee..hhhhhhhhhhhh...hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhh....eeee......hhhhhh..hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eee....eeee..eeeeeee.............hhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh....eeeee....hhhhhhhhheee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f97 B   3 GSEIFLASKRAAITYDTDPATGEPRAWLAPGGTGNVVAEQAGVLNISWIASADSEDDRRASALNPDGVTMELREILVRLIRHDPAVFRNVQNFMTANLMWAANNYGWDRWTQPSFGSDAREGWADFGRFTRDFADAILKSSAQSADPVYLVHDYQLVGVPALLREQRPDAPILLFVHIPWPSADYWRILPKEIRTGILHGMLPATTIGFFADRWCRNFLESVADLLPDARIDREAMTVEWRGHRTRLRTMPLGYSPLTQLPEGIEEWADGHRLVVHSGRTDPIKNAERAVRAFVLAARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGSDTVRIDNDNDVNHTIACFRRADLLIFNSTVDGQNLSTFEAPLVNERDADVILSETCGAAEVLGEYCRSVNPFDLVEQAEAISAALAAGPRQRAEAAARRRDAARPWTLEAWVQAQLDGLAADHAARTAT 481
                                    12        22        32        42        52        62        72 ||     85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
                                                                                                  74|                                                                                                                                                                                      263|                                                                                                                                                                                                                   
                                                                                                   78                                                                                                                                                                                       270

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3vdm	CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE WHICH CATALYZES NON-GLYCOSIDIC C-N COUPLING IN VALIDAMYCIN A BIOSYNTHESIS
3vdn	CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX WITH GDP, 2.55 ANGSTROM RESOLUTION
4f96	CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX WITH GDP, 2.15 ANGSTROM RESOLUTION
4f9f	CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX WITH GDP AND TREHALOSE

Description