[English] 日本語
Yorodumi
- PDB-1j6t: COMPLEX OF ENZYME IIAMTL AND THE HISTIDINE-CONTAINING PHOSPHOCARR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j6t
TitleCOMPLEX OF ENZYME IIAMTL AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE
Components
  • PTS SYSTEM, MANNITOL-SPECIFIC IIABC COMPONENT
  • Phosphocarrier protein HPr
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER)
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannitol phosphotransferase / protein-N(PI)-phosphohistidine-mannitol phosphotransferase system transmembrane transporter activity / protein-phosphocysteine-mannitol phosphotransferase system transporter activity / mannitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system ...protein-Npi-phosphohistidine-D-mannitol phosphotransferase / protein-N(PI)-phosphohistidine-mannitol phosphotransferase system transmembrane transporter activity / protein-phosphocysteine-mannitol phosphotransferase system transporter activity / mannitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / kinase activity / phosphorylation / plasma membrane / cytosol
Similarity search - Function
Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 ...Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / Phosphotransferase system, EIIC / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Phosphotransferase/anion transporter / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / PTS system mannitol-specific EIICBA component / Phosphocarrier protein HPr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsClore, G.M. / Cornilescu, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Solution Structure of the Phosphoryl Transfer Complex between the Cytoplasmic A Domain of the Mannitol Transporter IImannitol and HPr of the Escherichia coli Phosphotransferase System
Authors: Cornilescu, G. / Lee, B.R. / Cornilescu, C.C. / Wang, G. / Peterkosfky, A. / Clore, G.M.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / diffrn ...atom_site / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_refine / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / struct_asym
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_PDB_model_num / _atom_site.type_symbol / _pdbx_nmr_refine.details / _pdbx_nmr_spectrometer.model / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.PDB_model_num / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS SYSTEM, MANNITOL-SPECIFIC IIABC COMPONENT
B: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5573
Polymers25,4782
Non-polymers791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area10990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 200REGULARIZED MEAN STRUCTURES
Representative

-
Components

#1: Protein PTS SYSTEM, MANNITOL-SPECIFIC IIABC COMPONENT / IIAMTL / EIIA-MTL / PHOSPHOTRANSFERASE ENZYME II / A DOMAIN COMPONENT


Mass: 16348.547 Da / Num. of mol.: 1 / Fragment: EIIA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00550
#2: Protein Phosphocarrier protein HPr / HPR / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: IPAP EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN A NEMATIC PHASE OF A 4-5% PEG/HEXANOL (SURFACTANT TO ALCOHOL RATION OF 0.96)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
1313D, 4D HETERONUCLEAR SEPARATED, FILTERED NOE EXPTS
141IPAP EXPERIMENTS FOR DIPOLAR COUPLINGS

-
Sample preparation

Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 7.0 / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE DMXBrukerAVANCE DMX5001
Bruker AVANCE DMXBrukerAVANCE DMX6002
Bruker AVANCE DRXBrukerAVANCE DRX7503
Bruker AVANCE DRXBrukerAVANCE DRX8004
Bruker AVANCE DRXBrukerAVANCE DRX8005

-
Processing

NMR softwareName: X-PLOR_NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA / Classification: refinement
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302; (CLORE & BEWLEY (2002) J.MAGN.RESON. 154, 329-335) THE ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302; (CLORE & BEWLEY (2002) J.MAGN.RESON. 154, 329-335) THE TARGET FUNCTIONS COMPRISES TERMS FOR THE NOE RESTRAINTS, THE SIDECHAIN TORSION ANGLE RESTRAINTS, THE BACKBONE TORSION ANGLE RESTRAINTS FOR 4 VARIABLE REGIONS OF IIAMTL, THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999), AND A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129- 136). THE STARTING COORDINATES COME FROM THE X-RAY STRUCTURES (WITH PROTONS ADDED) OF E. COLI HPR (1POH, JIA ET AL. (1993) J.BIOL.CHEM. 268, 22940-22501, RESOLUTION 1.5 A); AND IIAMTL (MOLECULE D OF 1A3A, VAN MONTFORT ET AL. STRUCTURE 5, 217-225 (1998); RESOLUTION 1.8A). SEVERAL DIFFERENT INITIAL ORIENTATIONS OF THE TWO PROTEINS WERE EMPLOYED WITH THE CA-CA DISTANCE BETWEEN THE ACTIVE SITE HISTIDINES RANGING FROM 28 TO 95 A, INCLUDING ORIENTATIONS WHERE THE TWO ACTIVE SITE HISTIDINES ARE NOT OPPOSED AND WHERE HPR IS DIRECTED TOWARDS THE FACE OF IIAMTL OPPOSITE TO THE IIAMTL ACTIVE SITE. THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS (EXCLUDING THE FOUR VARIABLE REGIONS OF IIAMTL: RESIDUES 51-54, 66-78, 91-96 AND 104-110) ARE TREATED AS RIGID BODIES THROUGHOUT WITH IIAMTL HELD FIXED, HPR ALLOWED TO ROTATE AND TRANSLATE, AND THE AXIS OF THE DIPOLAR COUPLING ALIGNMENT TENSOR FREE TO ROTATE. THE INTERFACIAL SIDECHAINS, AS WELL AS THE BACKBONE AND SIDECHAINS OF THE FOUR VARIABLE REGIONS OF IIAMTL, ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM. ALSO NOTE THAT GLU59 AND HIS111 ARE REFINED IN TWO ALTERNATE CONFORMATIONS. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS (EXCLUDING THE FOUR VARIABLE REGIONS OF IIAMTL) PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE ORIENTATION OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES OF HPR AND IIAMTL. RESIDUE NUMBERING: IIAMTL: 4-147 (RESIDUES 1-3 ARE DISORDERED IN SOLUTION AND NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THE CRYSTAL STRUCTURE OF THE FREE PROTEIN). HPR: 301-385 (CORRESPONDING TO RESIDUES 1-85). PHOSPHATE: RESIDUE 200 THREE SETS OF COORDINATES ARE GIVEN: MODEL 1: RESTRAINED REGULARIZED MEAN COORDINATES OF THE UNPHOSPHORYLATED HPR-IIAGLC COMPLEX SOLVED ON THE BASIS OF 107 INTERMOLECULAR INTERPROTON DISTANCE DISTANCE RESTRAINTS, 105 INTRAMOLECULAR DISTANCE RESTRAINTS (RELATING TO INTERFACIAL SIDECHAINS, AS WELL AS THE FOUR VARIABLE REGIONS OF IIAMTL), 70 INTERFACIAL SIDECHAIN TORSION ANGLE RESTRAINTS, 62 TORSION ANGLE RESTRAINTS FOR THE VARIABLE REGIONS OF IIAMTL, AND 528 RESIDUAL DIPOLAR COUPLINGS. CROSS-VALIDATION WAS USED FOR THE DIPOLAR COUPLINGS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012). MODEL 2: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE DISSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAMTL COMPLEX. EXPERIMENTAL RESTRAINTS ARE IDENTICAL TO THOSE USED FOR MODEL 3, BUT COVALENT GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL GEOMETRY. THE STRUCTURE IS DERIVED FROM MODEL 3 BY RESTRAINED MINIMIZATION. THE N-P BOND LENGTHS ARE RESTRAINED TO 3 A. THE CA-CA DISTANCE BETWEEN HIS315 (HPR) AND HIS65 (IIAMTL) REMAINS ESSENTIALLY UNCHANGED FROM MODEL 3, BUT THE ND1-NE2 DISTANCE BETWEEN HIS315 AND HIS65 IS REDUCED TO 6 A, WITH ESSENTIALLY IDEALIZED GEOMETRY OF THE PHOSPHORYL TRANSITION STATE. THE ND1-NE2 DISTANCE CORRESPONDS TO A DISSOCIATIVE TRANSITION STATE. THE RMS DIFFERENCE BETWEEN THE MEAN STRUCTURE OF THE UNPHOSPHORYLATED COMPLEX (MODEL 3) AND THE TRANSITION STATE COMPLEX IS 0.2 A FOR BACKBONE COORDINATES IMMEDIATELY ADJACENT TO THE ACTIVE SITE HISTIDINES (RESIDUES 64-66 AND RESIDUES 316-317). THE REMAINING BACKBONE COORDINATES DO NOT SHIFT. MODEL 3: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAGLC COMPLEX. CALCULATED LIKE MODEL 2 BUT WITH THE N-P BOND LENGTHS RESTRAINED TO 2A. THE STRUCTURE IS DERIVED FROM MODEL 1 BY RESTRAINED MINIMIZATION. THE RMS DIFFERENCE BETWEEN THE MEAN STRUCTURES OF THE UNPHOSPHORYLATED COMPLEX (MODEL 1) AND THE TRANSITION STATE COMPLEX IS 0.4 A FOR BACKBONE COORDINATES IMMEDIATELY ADJACENT TO THE ACTIVE SITE HISTIDINES (RESIDUES 64-66 AND RESIDUES 316-317). THE REMAINING BACKBONE COORDINATES DO NOT SHIFT. HPR-IIAMTL COMPLEX DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.006 A, ANGLES 0.82 DEG, IMPROPER TORSIONS 0.97 DEG RMS DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.007 A RMS DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.26 DEG. RMS DEVIATIONS FROM BACKBONE TORSION ANGLE RESTRAINTS: 1.2 DEG. DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): HPR IIAMTL NH 19.1% 19.2% CaH 25.9% 18.7% NC' 34.0% 32.1% [NOTE ONE ALIGNMENT TENSOR IS USED FOR THE NH DIPOLAR COUPLINGS (FOR BOTH HPR AND IIAMTL), AND ANOTHER FOR THE CAH AND NC' DIPOLAR COUPLINGS (FOR BOTH HPR AND IIAMTL), SINCE THE LATTER SET OF DIPOLAR COUPLINGS WERE OBTAINED FROM A DIFFERENT BATCH OF PEG/HEXANOL THAN THE FORMER. THE ORIENTATION OF THE TWO ALIGNMENT TENSORS DIFFERS BY ONLY 1.9 DEG. NOTE THE ALIGNMENT TENSORS FOR HPR AND IIAMTL ARE THE SAME. FOR REFERENCE THE DIPOLAR COUPLING R-FACTORS FOR THE FREE STRUCTURES (USING INDIVIDUAL ALIGNMENT TENSORS FOR THE TWO PROTEINS) ARE 21.3% (NH), 21.1% (CaH), 33.6% (NC') FOR THE X-RAY STRUCTURE OF HPR, AND 19.2% (NH), 18.0% (CaH) AND 32.0% (NC') FOR THE RESTRAINED REGULARIZED MEAN STRUCTURE OF IIAMTL IN THE COMPLEX].
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURES / Conformers calculated total number: 200 / Conformers submitted total number: 3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more