1BYU Protein Project

Jay R. Leister

Overview
This web site provides information about the Canine GDP-Ran protein (PDB Id: 1BYU). This site has been produced by Jay Leister (JayLeister@Hotmail.com).

1BYU is a transport protein composed of the GTP-Binding Protein Ran molecule. A transport protein is a transmembrane protein that helps a certain substance or class of closely related substance to cross the membrane. It's function is required for the import of protein into the nucleus and also for rna export. Transactivation decreases as the poly-gln length within ar increases. It is involved in chromatin condensation and control of cell cycle (by similarity). It also enhances ar-mediated transactivation. Gtp-binding protein is involved in nucleocytoplasmic transport.

This protein is part of the RAC family and the RAN Subfamily which also includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. The release date of this protein is December 1998.

Please see the following links on this web page:

Expermintal Data

Ligand Information

SCOP Information

CATH Information

Structural Neighbors

Secondary Structures

Additional Links

Expermintal Data (back to menu)

Compound Molecule: Gtp-Binding Protein Ran
Chain: A, B
Fragment: All
Synonym: Tc4
Engineered: Yes

Source
Organism_scientific: Canis Familiaris
Strain: Bl21(De3)
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet

Classification
Transport Protein

Symmetry Space Group: P 1 21 1

R_factor
0.176

Crystal Cell
(unit cell dimensions)

length a length b lenght c
angle alpha
angle beta
beta gamma

60.790
60.433
61.200
90.00
101.67
90.00

Method
X-Ray Diffraction resolution 2.15 Å

Resolution
(of electron density map)
2.15 Å

Enzyme

Ligand
(HET groups)
MG - MAGNESIUM ION (formula: "2(Mg)") (2 atoms)
GDP - GUANOSINE-5'-DIPHOSPHATE (formula: "2(C10H15N5O11P2)") (56 atoms)

Related structures
by homologous chain: 1IBR, 3RAN

Similarity
Belongs to the ran family in the ras superfamily

Subunit
The interaction with ar is inversely correlated with the poly-gln length. Also forms a complex with chc1 and interacts with the ar n-terminal poly-gln region. Monomer.

Post-translat
modifications The n-terminus is blocked.

Tissue
In mouse, expressed in a variety of tissues, including testis

Subcellular loc
Nuclear; becomes dispersed throughout the cytoplasm during mitosis.

Genes
ARA24, LPS, RAN, RASL2-8 (H. sapiens)

Polymer Chains
A, B

Residues
432

Atoms
3594

Function
Required for the import of protein into the nucleus and also for rna export. Transactivation decreases as the poly-gln length within ar increases. Involved in chromatin condensation and control of cell cycle (by similarity). Enhances ar-mediated transactivation. Gtp-binding protein involved in nucleocytoplasmic transport.

Disease
Popliteal pterygium syndrome
van der Woude syndrome

Primary Citations (and authors)
Stewart, M., Kent, H. M., McCoy, A. J.: The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2). J Mol Biol 284 pp. 1517 (1998)
[ Medline]

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Ligands (back to menu)

        A ligands is a small molecules that bind to a receptor site of a protein. This protein, 1byu, contains two ligands, MG and GDP.
        Here is a Rasmol graphic that highlights the ligands and their location: MG in green and GDP in red.

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SCOP Information (back to menu)

SCOP protein identification: CANINE GDP-RAN also 'Ran from Dog (Canis familiaris)'.

Lineage:

Root: scop

Class: Alpha and beta proteins (a/b)

Mainly parallel beta sheets (beta-alpha-beta units)

Fold: P-loop containing nucleotide triphosphate hydrolases

3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes

Superfamily: P-loop containing nucleotide triphosphate hydrolases

division into families based on beta-sheet topologies

A few graphic Family Examples from this superfamily:

Nucleotide and nucleoside kinases (25) - parallel beta-sheet of 5 strands, order 23145

Gluconate kinase

Family: G proteins

core: mixed beta-sheet of 6 strands, order 231456; strand 2 is antiparallel to the rest

Protein Domains

G Protein graphics

Protein: Ran

Species: Dog (Canis familiaris)

PDB Entry Domain

3ran - complexed with gdp, mg; mutant
Contains: chain a, chain b, chain c, chain d

1byu - complexed with gdp, mg
Contains: chain a, chain b

1qg2 - complexed with gdp, mo4; mutant
Contains: chain a

1qg4 - complexed with gdp, mo4; mutant
Contains: chain a, chain b

1a2k - complexed with gdp, mg, so4
Contains: chain c, chain d, chain e

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CATH Information (back to menu)
    (CATH - Protein Structure Classification for Class, Architecture, Topology and Homolgy)

CATH Domains: 1byuA0 and 1byuB0

Domains

        Domain     CATH code (superfamily)         Length         Image
        1byuA0     3.40.50.300                             202


        1byuB0     3.40.50.300                           215


Class for both: Alpha Beta

Class representative: 1rthA1

Mainly parallel beta sheets (beta-alpha-beta units)

Architecture: 3-Layer(aba) Sandwich

Architecture representative: 1div01

Topology: Rossmann fold

Topology representive: 2minB2

Homology: P-loop containing nucleotide triphosphate hydrolases (3.40.50.300)

Homologous superfamily representative: 1efuA1

Sequence family (Transport Protein): 3.40.50.300.10

Sequence family representative: See domain 1byuA0 above

Non-identical relatives (Transport Protein) : 3.40.50.300.10.1

Non-identical representative: See domain 1byuA0 above

Fold relatives: There are 354 other non-identical relatives within this fold group. See the table link.

Fold: P-loop containing nucleotide triphosphate hydrolases

3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes

Homologous Superfamily 3.40.50.300

Superfamily: P-loop containing nucleotide triphosphate hydrolases

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Structural Neighbors (back to menu)

There were 1272 structural neighbors selected from PDB for 1BYU. I selected 'Ran-Rcc1-So4 Complex' (1I2M) for the comparison.
As these comparison shows, the structures and sequence align very closely. I see only 2 not-aligned residues for 1I2M, which are too light to display here.
For better detail see link.

CLUSTAL W (1.82) Multiple Sequence Alignments (or click here)

Sequence format is Pearson
Sequence 1: 1BYU_A          216 aa
Sequence 2: 1I2M_A          216 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 99
Guide tree        file created:   [/ebi/extserv/old-work/869597.858957.dnd]
Start of Multiple Alignment
There are 1 groups
Aligning...
Group 1: Sequences:   2      Score:4707
Alignment Score 1362
CLUSTAL-Alignment file created [/ebi/extserv/old-work/869597.858957.aln]

CLUSTAL W (1.82) multiple sequence alignment

1BYU_A         MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVPTLGVEVHPLVFHTNRGPIK 60
1I2M_A          MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK 60
                ****************************************.*******************

1BYU_A         FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC 120
1I2M_A          FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC 120
                ************************************************************

1BYU_A         GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP 180
1I2M_A          GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP 180
                ************************************************************

1BYU_A         ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 216
1I2M_A          ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 216
                ************************************

        To view a list of all structural neighbors see:

For Chain 1BYU:A

For Chain 1BYU:B


Structural Neighbor Comparison

                    1byu Chain A                                                              Structural Neighbor - 1I2M


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Secondary Structures (back to menu)
Chain 1BYU:A
Compound    GTP-Binding Protein Ran
Type    Protein
Molecular Weight    24434
Number of Residues    216
Number of Alpha    8     Content of Alpha    28.70
Number of Beta    7     Content of Beta    22.69

Sequence and secondary structure
   1 MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV PTLGVEVHPL
                             E EEEEEEE TT SSHHHHHTTB HHHHHT EEE TTTTEEEEEE

51 VFHTNRGPIK FNVWDTAGQE KFGGLRDGYY IQAQCAIIMF DVTSRVTYKN
    EEEETTEEEE EEEEEE STT SSS    HHHH TT SEEEEEE ETTTHHHHHT

101 VPNWHRDLVR VCENIPIVLC GNKVDIKDRK VKAKSIVFHR KKNLQYYDIS
   HHHHHHHHHH HH S EEEEE EE TTSSS   S GGGGHHHH HTT EEEE B

151 AKSNYNFEKP FLWLARKLIG DPNLEFVAMP ALAPPEVVMD PALAAQYEHD
     GGGTBTTTHH HHHHHHHHHT TT BSB    B    SS        HHHHHHHHHH

201 LEVAQTTALP DEDDDL
     HHHHH

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Chain 1BYU:B
Compound GTP-Binding Protein Ran
Type Protein
Molecular Weight 24434
Number of Residues 216
Number of Alpha 8 Content of Alpha 29.63
Number of Beta 7 Content of Beta 24.07

Sequence and secondary structure
1 MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV PTLGVEVHPL
      TTTS   E EEEEEEE TT SSHHHHHTTB HHHHHT EEE TTTTEEEEEE

  51 VFHTNRGPIK FNVWDTAGQE KFGGLRDGYY IQAQCAIIMF DVTSRVTYKN
     EEEETTEEEE EEEEEE SGG GTS   HHHH TT EEEEEE ETTTHHHHHT

101 VPNWHRDLVR VCENIPIVLC GNKVDIKDRK VKAKSIVFHR KKNLQYYDIS
     HHHHHHHHHH HH S EEEEE EE TTSSS   S HHHHTTT   SSEEEEEEE

151 AKSNYNFEKP FLWLARKLIG DPNLEFVAMP ALAPPEVVMD PALAAQYEHD
     GGGTBTTTHH HHHHHHHHHT    TT BSS      B   SS    HHHHHHHHHH

201 LEVAQTTALP DEDDDL
     HHHHHHHHS   TT

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Also see: HSSP - HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS
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Additional 1BYU Links (back to menu)

PDBsum - A database of the known 3D structures of proteins and nucleic acids

OCA

Procheck

IMB - Image Library of Biological Macromolecule