3iss

Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	PHOSPHITE ION × 1 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–418； UniProt 1–418 Author chain B； PDBConstruct 1–418； UniProt 1–418 Author chain C； PDBConstruct 1–418； UniProt 1–418 Author chain D； PDBConstruct 1–418； UniProt 1–418 Author chain E； PDBConstruct 1–418； UniProt 1–418 Author chain F； PDBConstruct 1–418； UniProt 1–418 Author chain G； PDBConstruct 1–418； UniProt 1–418 Author chain H； PDBConstruct 1–418； UniProt 1–418 Author chain I； PDBConstruct 1–418； UniProt 1–418 Author chain J； PDBConstruct 1–418； UniProt 1–418 Author chain K； PDBConstruct 1–418； UniProt 1–418 Author chain L； PDBConstruct 1–418； UniProt 1–418

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3iss
Deposition date deposition_date	2009-08-27
Structure title title	Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli
Keywords keywords	Protein-Ligand, Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3iss__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3iss__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3iss__assembly_9__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.56 Å
Rg (electron density)	21.53 Å
Total Rg	22.28 Å
Atom count	3181
Residues	418
Excluded volume	56755 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3iss__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3iss__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3iss__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3iss__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3iss__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3iss__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3iss__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3iss__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3iss__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3iss__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3iss__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3iss__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Molecular weight formula_weight	44743.4 kDa
EC 编号 ec_number	2.5.1.7
Mutation mutation	N67D
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	39025

MDKFRVQGPTKLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDVDTSMKLLSQLGAKVERDGSVHIDARDVNVFCAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCTIGARPVDLHISGLEQLGATIKLEEGYVKASVDGRLKGAHIVMDKVSVGATVTIMCAATLAEGTTIIENAAREPEIVDTANFLITLGAKISGQGTDRIVIEGVERLGGGVYRVLPDRIETGTFLVAAAISRGKIICRNAQPDTLDAVLAKLRDAGADIEVGEDWISLDMHGKRPKAVNVRTAPHPAFPTDMQAQFTLLNLVAEGTGFITETVFENRFMHVPELSRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKG

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHITE ION
Molecular weight formula_weight	79.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
Molecular weight formula_weight	677.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	853

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3issa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3isse_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d3issl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

CATH v4.4 (24 domains)

Domain ID domain_id	3issA01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issA02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issB01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issB02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issC01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issC02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issD01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issD02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issE01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issE02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issF01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issF02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issG01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issG02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issH01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issH02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issI01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issI02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issJ01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issJ02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issK01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issK02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issL01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	3issL02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

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Unit-cell length a length_a	84.510 Å
Unit-cell length b length_b	120.910 Å
Unit-cell length c length_c	139.730 Å
Unit-cell angle α angle_alpha	111.52 °
Unit-cell angle β angle_beta	104.44 °
Unit-cell angle γ angle_gamma	90.19 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.478 Å
R factor r_factor	0.2231
R_work r_work	0.2215
R_free r_free	0.2537

Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli

1. Protein Identity and Related Structures Protein Identity & Related Structures

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3iss__assembly_9__model_1

3iss__assembly_9__model_1 | I(q)

3iss__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli

1. Protein Identity and Related Structures Protein Identity & Related Structures

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3iss__assembly_9__model_1

3iss__assembly_9__model_1 | I(q)

3iss__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)