5VYT - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE WBKC N-FORMYLTRANSFERASE (F142A VARIANT) FROM BRUCELLA MELITENSIS

Authors :   A. S. Riegert, D. P. Chantigian, J. B. Thoden, H. M. Holden

Date :   26 May 17 (Deposition) - 05 Jul 17 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Brucellosis, Deoxysugar, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Riegert, D. P. Chantigian, J. B. Thoden, P. A. Tipton, H. M. Holden
Biochemical Characterization Of Wbkc, An N-Formyltransferas From Brucella Melitensis.
Biochemistry 2017
PubMed-ID: 28636341 | Reference-DOI: 10.1021/ACS.BIOCHEM.7B00494

Molecule 1 - GDP-MANNOSE 4,6-DEHYDRATASE / GDP-4-AMINO-4,6-DIDEOXY-D- MANNOSE FORMYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.2.-, 4.2.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Gene	:	BMEI1418
	Mutation	:	YES
	Organism Scientific	:	BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN 16M / ATCC 23456 / NCTC 10094)
	Organism Taxid	:	224914
	Strain	:	16M / ATCC 23456 / NCTC 10094

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FON	4	Ligand/Ion	N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
3	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FON	2	Ligand/Ion	N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FON	2	Ligand/Ion	N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:87 , ARG A:88 , SER A:89 , LEU A:90 , ILE A:91 , ASN A:105 , ASP A:139 , ASN A:141 , ALA A:142 , ASP A:143 , HOH A:412	binding site for residue FON A 301
2	AC2	SOFTWARE	ARG A:45 , ARG A:88 , ASN A:118 , VAL A:120 , ALA A:161 , PHE A:165 , LEU A:203 , MET A:225 , PHE A:227 , PHE A:230 , PRO A:231 , HOH A:424	binding site for residue GDP A 302
3	AC3	SOFTWARE	TYR B:87 , ARG B:88 , SER B:89 , LEU B:90 , ILE B:91 , ASN B:105 , ASP B:139 , ASN B:141 , ALA B:142 , ASP B:143 , HOH B:414	binding site for residue FON B 301
4	AC4	SOFTWARE	ARG B:45 , ARG B:88 , ASN B:118 , ALA B:161 , LEU B:203 , MET B:225 , PHE B:227 , PHE B:230 , HOH B:416 , HOH B:440	binding site for residue GDP B 302
5	AC5	SOFTWARE	TYR C:87 , SER C:89 , LEU C:90 , ILE C:91 , ASN C:105 , MET C:138 , ASP C:139 , ASN C:141 , ALA C:142 , ASP C:143 , ARG C:201 , HOH C:410	binding site for residue FON C 301
6	AC6	SOFTWARE	ARG C:45 , ARG C:88 , ASN C:118 , VAL C:120 , ALA C:161 , PHE C:165 , LEU C:203 , MET C:225 , PHE C:227 , PHE C:230 , PRO C:231 , HOH C:401 , HOH C:435 , HOH C:438	binding site for residue GDP C 302
7	AC7	SOFTWARE	TRP D:213	binding site for residue CL C 303
8	AC8	SOFTWARE	TYR D:87 , ARG D:88 , SER D:89 , LEU D:90 , ILE D:91 , LEU D:96 , ASN D:105 , MET D:138 , ASP D:143 , ARG D:201 , HOH D:412	binding site for residue FON D 301
9	AC9	SOFTWARE	ARG D:45 , ARG D:88 , ASN D:118 , MET D:225 , PHE D:230 , HOH D:405 , HOH D:408 , HOH D:420 , HOH D:438 , HOH D:447	binding site for residue GDP D 302

(no "SS Bond" information available for 5VYT)

Asymmetric Unit

No.	Residues
1	Leu A:111	-	Pro A:112
2	Pro A:228	-	Pro A:229
3	Leu B:111	-	Pro B:112
4	Pro B:228	-	Pro B:229
5	Leu C:111	-	Pro C:112
6	Pro C:228	-	Pro C:229
7	Leu D:111	-	Pro D:112
8	Pro D:228	-	Pro D:229

(no "SAP(SNP)/Variant" information available for 5VYT)

(no "PROSITE Motif" information available for 5VYT)

(no "Exon" information available for 5VYT)

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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhh.eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee...hhhhhh.....hhhhhhhhhhhhh......ee....ee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyt A   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIYYVPSIDIYRSL 253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     ||245        
                                                                                                                                                                                                                                                                     237|           
                                                                                                                                                                                                                                                                      242

Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeehhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh.......eee....eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vyt B   1 MAIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVPSIDIYRS 252
                                    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

Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh......eeeee..eeeee.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyt C   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVPSIDIYRSLMRGI 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain D from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhh.eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhh.......eeeee..eeeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyt D   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDDTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVPSIDIYRSLM 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       144       154       164       174       184       194       204       214       224       234       244       254
                                                                                                                                                                   139|                                                                                                               
                                                                                                                                                                    143

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5VYT)

(no "CATH Domain" information available for 5VYT)

(no "Pfam Domain" information available for 5VYT)

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		Leu D:111 - Pro D:112	[ RasMol ]
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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