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(-) Description

Title :  CRYSTAL STRUCTURE OF BRANCHING ENZYME FROM CYANOTHECE SP. ATCC 51142 IN COMPLEX WITH MALTOHEXAOSE
 
Authors :  R. Suzuki, E. Suzuki
Date :  08 Aug 16  (Deposition) - 22 Feb 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Branching Enzyme, Glycoside Hydrolase Family 13, Cyanobacteria, Starch, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hayashi, R. Suzuki, C. Colleoni, S. G. Ball, N. Fujita, E. Suzuki
Bound Substrate In The Structure Of Cyanobacterial Branchin Enzyme Supports A New Mechanistic Model
J. Biol. Chem. V. 292 5465 2017
PubMed-ID: 28193843  |  Reference-DOI: 10.1074/JBC.M116.755629
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1,4-ALPHA-GLUCAN BRANCHING ENZYME GLGB
    Atcc: 51142
    Chains: A
    EC Number: 2.4.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLGB, GLGB1, CCE_2248
    Organism Scientific: CYANOTHECE SP. (STRAIN ATCC 51142)
    Organism Taxid: 43989
    Strain: ATCC 51142

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 40)

Asymmetric/Biological Unit (3, 40)
No.NameCountTypeFull Name
1GLC37Ligand/IonALPHA-D-GLUCOSE
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:576 , ARG A:580 , PRO A:622 , GLN A:625 , TYR A:714 , GLY A:715binding site for residue GOL A 838
02AC2SOFTWAREHIS A:19 , GLU A:23 , HIS A:516 , LEU A:519 , ASP A:520 , GLU A:556 , LYS A:561 , LYS A:567binding site for residue GOL A 839
03AC3SOFTWAREASP A:612 , HOH A:940 , HOH A:946 , HOH A:958 , HOH A:989 , HOH A:996binding site for residue MG A 840
04AC4SOFTWAREASP A:8 , ARG A:216 , PRO A:217 , VAL A:282 , GLU A:284 , PRO A:322 , PHE A:323 , ASP A:324 , SER A:326 , TRP A:327 , GLN A:330 , ASP A:373 , TRP A:399 , GLY A:400 , TRP A:610binding site for Poly-Saccharide residues GLC A 801 through GLC A 806
05AC5SOFTWAREASP A:8 , TRP A:147 , ASN A:150 , TYR A:175 , ARG A:216 , PRO A:217 , VAL A:282 , GLU A:284 , PRO A:322 , PHE A:323 , ASP A:324 , GLN A:330 , ASP A:373 , TRP A:399 , GLY A:400 , GLY A:407 , ARG A:408 , HIS A:409 , GLU A:410 , TRP A:610 , GLC A:801binding site for Poly-Saccharide residues GLC A 807 through GLC A 810
06AC6SOFTWARETRP A:147 , ASN A:150 , TRP A:163 , TYR A:175 , LYS A:192 , GLU A:204 , GLU A:214 , ARG A:408 , GLU A:410 , GLC A:807binding site for Poly-Saccharide residues GLC A 811 through GLC A 813
07AC7SOFTWAREARG A:59 , TRP A:163 , GLU A:214 , LEU A:247 , PHE A:476 , SER A:496 , ARG A:497 , PRO A:498 , VAL A:499 , TYR A:500 , ASP A:501 , GLY A:505 , PHE A:506 , ASN A:547 , GLC A:811binding site for Poly-Saccharide residues GLC A 814 through GLC A 820
08AC8SOFTWAREARG A:59 , LEU A:247 , PHE A:476 , SER A:496 , ARG A:497 , PRO A:498 , VAL A:499 , TYR A:500 , ASP A:501 , GLY A:505 , PHE A:506 , ASN A:547 , ASP A:657 , HIS A:663 , HIS A:692 , TYR A:693 , ARG A:694 , PHE A:732 , HIS A:733 , GLC A:814binding site for Poly-Saccharide residues GLC A 821 through GLC A 824
09AC9SOFTWAREASP A:657 , HIS A:663 , HIS A:692 , TYR A:693 , ARG A:694 , GLU A:705 , PHE A:707 , ASN A:708 , ALA A:711 , GLN A:713 , TYR A:714 , ASN A:718 , GLY A:720 , ASN A:721 , LEU A:722 , GLY A:723 , LYS A:725 , PHE A:732 , HIS A:733 , GLC A:821binding site for Poly-Saccharide residues GLC A 825 through GLC A 830
10AD1SOFTWAREASP A:571 , TRP A:573 , GLN A:574 , PRO A:687 , PRO A:689 , GLU A:705 , PHE A:707 , ASN A:708 , ALA A:711 , GLN A:713 , TYR A:714 , SER A:717 , ASN A:718 , MET A:719 , GLY A:720 , ASN A:721 , LEU A:722 , GLY A:723 , GLC A:825binding site for Poly-Saccharide residues GLC A 831 through GLC A 834
11AD2SOFTWAREASN A:137 , GLY A:138 , THR A:537 , PHE A:538 , MET A:540 , ASP A:571 , TRP A:573 , GLN A:574 , TRP A:655 , CYS A:658 , PRO A:687 , PRO A:689 , SER A:717 , MET A:719 , GLC A:831binding site for Poly-Saccharide residues GLC A 835 through GLC A 837

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GQV)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:216 -Pro A:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GQV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GQV)

(-) Exons   (0, 0)

(no "Exon" information available for 5GQV)

(-) Sequences/Alignments

Asymmetric/Biological 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:755
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhh.eeeeeee....eeeeeeee.....eeeeeehhhheeee.ee.....eeeeeee.......eeeeee..eeeeee..........hhhhhhhhhhh...hhhhh.eeeeeee..eeeeeeeee.....eeeeee.hhh..hhhhh.eee...eeeeeee......eeeeeee.....eeee...............ee..hhhhh....hhhhhhhhhh.hhhhh..eeeee......eee....eee..eee...........eee.hhhhhhhhhhhhhhhhh..eeee...ee..hhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh..eeeeee....ee..................hhhhhee....ee.....hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhh...................hhhhhhhhhhhhhhhhhhh...eeee...........hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh.eeeee..hhhh.eeeeee...hhhh.eeeeee.....eeeeeeee....eeeeeee..hhhhh........eee.eeeee..eeeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqv A   5 ISADQVNQIIYNLHHDPFEILGCHLLEEGKNTKKWVVRAYLPKAEAAWVIRPTERKEDPMNSVHHPNFFECIIETPELNHYQLKVKEGEHEKVIYDPYAFSSPYLTDEDIYLFSEGNHHRIYEKLGAHVGEINGVKGVYFAVWAPNARNVSVIGDFNNWDGREHQMRKRNYTIWELFVPEIGSGTVYKYEIKNSEGHIYEKSDPYGFYREVRPNTASIVVDIDNIYQWHDEEWLEKRRNSDPLKQPVSVYEVHLGSWLHGSSAEKMPLLNGEADPVIVSEWNPGARFLSYYELAEKLIPYVKDMGYTHIELLPIAEHPFDGSWGYQVTGFYSPTSRFGRPEDFMYFVDKCHENGIGVILDWVPGHFPKDSHGLAYFDGTHLYEHADPRIGEHKEWGTLVFNYGRHEVRNFLVANVLFWFDKYHVDGIRVDAVASMLYRNYLRKEGEWIANEYGGDEHIEAVSFIREVNTLLFEYFPGILSIAEESTEWEKVSRPVYDGGLGFNLKWDMGWMHDMLDYFNIDPYFRQYHQNNVTFSMLYYYNENFMLALSHDEIVHGKSNMLGKMPGDEWQKYANVRALFTYMYTHPGKKTMFMSMEFGQWSEWNVWGDLEWHLLQYEPHQQLKQFFTDLNALYQQEPALYTHDFEYHGFEWIDCNDNTHSVVSFLRRSDDPNDSLVVVCNFTPQPHSHYRIGVPEAGYYVELFNSDAKQYGGSNMGNLGGKWADEWSFHNKPYSLDLCLPPLAVLILKLDPTKVP 759
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GQV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GQV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GQV)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Arg A:216 - Pro A:217   [ RasMol ]  
 

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        B1WPM8_CYAA5 | B1WPM8: 5gqu 5gqw 5gqx

(-) Related Entries Specified in the PDB File

5gqu 5gqw 5gqx 5gqy 5gqz 5gr0 5gr1 5gr2 5gr3 5gr4 5gr5 5gr6