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1nvm

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

4-hydroxy-2-oxovalerate aldolase

Pseudomonas sp.

UniProt P51016

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 acetaldehyde dehydrogenase (acylating) × 2 （Q52060） MANGANESE (II) ION × 2 OXALATE ION × 2 SULFATE ION × 5 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 acetaldehyde dehydrogenase (acylating) × 2 （Q52060） MANGANESE (II) ION × 2 OXALATE ION × 2 SULFATE ION × 7 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 acetaldehyde dehydrogenase (acylating) × 4 （Q52060） MANGANESE (II) ION × 4 OXALATE ION × 4 SULFATE ION × 12 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1nvm 1nvm 1nvm

3 assemblies

View Construct and Data Evidence
UniProt name DMPG_PSEUF
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–345； UniProt 1–345 Author chain C； PDBConstruct 1–345； UniProt 1–345 Author chain E； PDBConstruct 1–345； UniProt 1–345 Author chain G； PDBConstruct 1–345； UniProt 1–345

acetaldehyde dehydrogenase (acylating)

Pseudomonas sp.

UniProt Q52060

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 4-hydroxy-2-oxovalerate aldolase × 2 （P51016） MANGANESE (II) ION × 2 OXALATE ION × 2 SULFATE ION × 5 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 4-hydroxy-2-oxovalerate aldolase × 2 （P51016） MANGANESE (II) ION × 2 OXALATE ION × 2 SULFATE ION × 7 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 4-hydroxy-2-oxovalerate aldolase × 4 （P51016） MANGANESE (II) ION × 4 OXALATE ION × 4 SULFATE ION × 12 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1nvm 1nvm 1nvm

3 assemblies

View Construct and Data Evidence
UniProt name Q52060_PSEUF
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–312； UniProt 1–312 Author chain D； PDBConstruct 1–312； UniProt 1–312 Author chain F； PDBConstruct 1–312； UniProt 1–312 Author chain H； PDBConstruct 1–312； UniProt 1–312

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_id1nvm
Deposition date deposition_date2003-02-04
Structure title titleCrystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
Keywords keywordsSequestered tunnel, substrate channeling, Bifunctional enzyme, LYASE-OXIDOREDUCTASE COMPLEX; LYASE/OXIDOREDUCTASE
Experimental Method methodX-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.

1nvm__assembly_1__model_1

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

Download this curve (.dat)

1nvm__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1nvm__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）39.06 Å
Rg (electron density)40.03 Å
Total Rg40.18 Å
Atom count9848
Residues1297
Excluded volume175350 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1nvm__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1nvm__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1nvm__assembly_3__model_1 octameric （8） 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 (8)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1nvma1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.7 — post-HMGL domain-like
Family Family familya.5.7.1 — DmpG/LeuA communication domain-like
Domain ID domain_idd1nvma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.5 — HMGL-like
Domain ID domain_idd1nvmb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nvmb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nvmc1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.7 — post-HMGL domain-like
Family Family familya.5.7.1 — DmpG/LeuA communication domain-like
Domain ID domain_idd1nvmc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.5 — HMGL-like
Domain ID domain_idd1nvmd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nvmd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nvme1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.7 — post-HMGL domain-like
Family Family familya.5.7.1 — DmpG/LeuA communication domain-like
Domain ID domain_idd1nvme2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.5 — HMGL-like
Domain ID domain_idd1nvmf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nvmf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nvmg1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.7 — post-HMGL domain-like
Family Family familya.5.7.1 — DmpG/LeuA communication domain-like
Domain ID domain_idd1nvmg2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.5 — HMGL-like
Domain ID domain_idd1nvmh1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nvmh2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like

CATH v4.4 (16 domains)

Domain ID domain_id1nvmA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1nvmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id1nvmB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nvmB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nvmC01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1nvmC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id1nvmD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nvmD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nvmE01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1nvmE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id1nvmF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nvmF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nvmG01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1nvmG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id1nvmH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nvmH02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
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7. Citations (2)