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Title :   CRYSTAL STRUCTURE OF E.COLI MENH Y85F MUTANT

Authors :   J. M. Johnston, E. N. Baker, Z. Guo, M. Jiang

Date :   01 Aug 12 (Deposition) - 08 May 13 (Release) - 04 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

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

Keywords :   Menaquinone Biosynthesis, Alpha Beta Hydrolase, 2-Succinyl-6-Hydroxy- 2, 4-Cyclohexadiene-1-Carboxylate Synthase, Menh Y85F Mutant, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Johnston, M. Jiang, Z. Guo, E. N. Baker
Crystal Structures Of E. Coli Native Menh And Two Active Site Mutants.
Plos One V. 8 61325 2013
PubMed-ID: 23637813 | Reference-DOI: 10.1371/JOURNAL.PONE.0061325

Molecule 1 - 2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE
	Chains	:	A, B, C
	EC Number	:	4.2.99.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B2263, JW2258, MENH, MENH_Y85FMUTANT, YFBB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	SHCHC SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 23)

No.	Name	Count	Type	Full Name
1	CL	7	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	13	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	-1	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:86 , LEU A:87 , ARG A:90 , EDO A:306 , HOH A:452 , HOH A:503 , HOH A:526 , HOH A:540	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	GLY A:60 , PHE A:61 , ASP A:62 , HOH A:401 , HOH A:529	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	ARG A:198 , ALA A:201 , PHE A:202 , TYR A:203 , HOH A:511	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	ALA A:7 , LYS A:8 , HIS A:9 , HOH A:493	BINDING SITE FOR RESIDUE SO4 A 304
05	AC5	SOFTWARE	TYR A:148 , ARG A:168 , ASN A:233	BINDING SITE FOR RESIDUE CL A 305
06	AC6	SOFTWARE	ARG A:124 , VAL A:152 , PHE A:213 , SO4 A:301 , HOH A:418	BINDING SITE FOR RESIDUE EDO A 306
07	AC7	SOFTWARE	SER B:86 , LEU B:87 , ARG B:90 , ARG B:124 , HOH B:437 , HOH B:441 , HOH B:534	BINDING SITE FOR RESIDUE SO4 B 301
08	AC8	SOFTWARE	ARG B:209 , ARG B:229	BINDING SITE FOR RESIDUE SO4 B 302
09	AC9	SOFTWARE	GLU B:163 , LEU B:167 , ARG B:236 , HOH B:491	BINDING SITE FOR RESIDUE SO4 B 303
10	BC1	SOFTWARE	HOH A:493 , ARG B:198 , ALA B:201 , PHE B:202	BINDING SITE FOR RESIDUE SO4 B 304
11	BC2	SOFTWARE	TYR B:148 , ARG B:168 , ASN B:233	BINDING SITE FOR RESIDUE CL B 305
12	BC3	SOFTWARE	HIS B:9 , TYR B:75 , PRO B:151 , VAL B:152 , LYS B:212	BINDING SITE FOR RESIDUE GOL B 306
13	BC4	SOFTWARE	GLN B:160	BINDING SITE FOR RESIDUE CL B 307
14	BC5	SOFTWARE	SER C:86 , ARG C:90 , ARG C:124 , HOH C:440 , HOH C:443 , HOH C:474 , HOH C:478 , HOH C:511	BINDING SITE FOR RESIDUE SO4 C 301
15	BC6	SOFTWARE	LYS C:8 , HIS C:9	BINDING SITE FOR RESIDUE SO4 C 302
16	BC7	SOFTWARE	ALA C:101 , GLY C:102	BINDING SITE FOR RESIDUE SO4 C 303
17	BC8	SOFTWARE	ARG C:236	BINDING SITE FOR RESIDUE SO4 C 304
18	BC9	SOFTWARE	SER C:0 , MET C:1 , ARG C:126 , GLN C:130	BINDING SITE FOR RESIDUE SO4 C 305
19	CC1	SOFTWARE	GLY B:173 , HOH B:429 , GLY C:173	BINDING SITE FOR RESIDUE CL C 306
20	CC2	SOFTWARE	TYR C:148 , ARG C:168 , ASN C:233	BINDING SITE FOR RESIDUE CL C 307
21	CC3	SOFTWARE	ARG C:69 , GLY C:99 , LEU C:100 , ALA C:101 , HOH C:505 , HOH C:512	BINDING SITE FOR RESIDUE GOL C 308
22	CC4	SOFTWARE	HOH C:491 , HOH C:499 , HOH C:533	BINDING SITE FOR RESIDUE CL C 309
23	CC5	SOFTWARE	LEU C:78 , ASP C:79	BINDING SITE FOR RESIDUE CL C 310

(no "SS Bond" information available for 4GEG)

(no "Cis Peptide Bond" information available for 4GEG)

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

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

(no "Exon" information available for 4GEG)

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
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Chain A from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee.......eeeee.........hhhhhh.....eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhh...eeeeeee..hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4geg A  -5 LVPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGFSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......eeeee.........hhhhhh.....eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee..hhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4geg B  -4 VPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGFSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILR 251
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee.......eeeee.........hhhhhh.....eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhh...eeeeeee..hhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4geg C  -5 LVPRGSMILHAQAKHGKPGLPWLVFLHGFSGDCHEWQEVGEAFADYSRLYVDLPGHGGSAAISVDGFDDVTDLLRKTLVSYNILDFWLVGFSLGGRVAMMAACQGLAGLCGVIVEGGHPGLQNAEQRAERQRSDRQWVQRFLTEPLTAVFADWYQQPVFASLNDDQRRELVALRSNNNGATLAAMLEATSLAVQPDLRANLSARTFAFYYLCGERDSKFRALAAELAADCHVIPRAGHNAHRENPAGVIASLAQILRF 252
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

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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 4GEG)

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	Cis Peptide Bonds
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Access by PDB/NDB ID
	4geg
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	MENH_ECOLI \| P37355
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	MENH_ECOLI \| P37355	:	4gdm 4gec 4mxd 4myd 4mys

4gdm	NATIVE E. COLI MENH STRUCTURE
4gec	E. COLI MENH R124A MUTANT STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 23)

Sites (23, 23)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (5, 5)

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