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(-) Description

Title :  CRYSTAL STRUCTURE OF BRANCHING ENZYME W610N MUTANT FROM CYANOTHECE SP. ATCC 51142 IN COMPLEX WITH MALTOHEPTAOSE
 
Authors :  R. Suzuki, E. Suzuki
Date :  08 Aug 16  (Deposition) - 22 Feb 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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
    Mutation: YES
    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, 42)

Asymmetric/Biological Unit (3, 42)
No.NameCountTypeFull Name
1GLC39Ligand/IonALPHA-D-GLUCOSE
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:572 , TRP A:573 , TYR A:576 , PRO A:622 , GLN A:625 , GLY A:715 , HOH A:1041binding site for residue GOL A 840
02AC2SOFTWAREHIS A:19 , GLU A:23 , HIS A:516 , ASP A:520 , GLU A:556 , LYS A:567 , HOH A:1239binding site for residue GOL A 841
03AC3SOFTWAREASP A:612 , HOH A:1039 , HOH A:1090 , HOH A:1138 , HOH A:1199 , HOH A:1212binding site for residue MG A 842
04AC4SOFTWAREASP A:8 , ARG A:216 , PRO A:217 , VAL A:282 , SER A:283 , GLU A:284 , PRO A:322 , PHE A:323 , ASP A:324 , SER A:326 , TRP A:327 , TYR A:329 , GLN A:330 , ASP A:373 , TRP A:399 , GLY A:400 , ASP A:434 , HIS A:554 , ASP A:555 , HIS A:559 , HOH A:972 , HOH A:978 , HOH A:981 , HOH A:1155 , HOH A:1158 , HOH A:1277binding site for Poly-Saccharide residues GLC A 801 through GLC A 807
05AC5SOFTWAREASP A:8 , ASN A:150 , TYR A:175 , ARG A:216 , PRO A:217 , VAL A:282 , SER A:283 , GLU A:284 , PRO A:322 , PHE A:323 , ASP A:324 , SER A:326 , TRP A:327 , TYR A:329 , GLN A:330 , ASP A:373 , TRP A:399 , GLY A:400 , GLY A:407 , ARG A:408 , HIS A:409 , GLU A:410 , HIS A:559 , GLC A:801 , HOH A:937 , HOH A:972 , HOH A:978 , HOH A:981 , HOH A:1001 , HOH A:1139 , HOH A:1158 , HOH A:1277binding site for Poly-Saccharide residues GLC A 808 through GLC A 811
06AC6SOFTWAREARG A:59 , ASN A:150 , TRP A:163 , TYR A:175 , LYS A:192 , GLU A:204 , GLU A:214 , ASN A:218 , ARG A:408 , GLU A:410 , PHE A:476 , GLU A:477 , 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:507 , ASN A:547 , GLC A:808 , HOH A:910 , HOH A:937 , HOH A:956 , HOH A:984 , HOH A:1001 , HOH A:1005 , HOH A:1139 , HOH A:1161 , HOH A:1167 , HOH A:1227binding site for Poly-Saccharide residues GLC A 812 through GLC A 821
07AC7SOFTWAREARG A:59 , TRP A:163 , GLU A:214 , ASN A:218 , PHE A:476 , GLU A:477 , 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:507 , ASN A:547 , ASP A:657 , ASN A:659 , HIS A:663 , HIS A:692 , TYR A:693 , ARG A:694 , PHE A:732 , HIS A:733 , GLC A:812 , HOH A:910 , HOH A:924 , HOH A:956 , HOH A:984 , HOH A:1005 , HOH A:1161 , HOH A:1167 , HOH A:1227binding site for Poly-Saccharide residues GLC A 822 through GLC A 825
08AC8SOFTWAREASP A:657 , HIS A:663 , SER A:691 , HIS A:692 , TYR A:693 , ARG A:694 , GLU A:705 , PHE A:707 , ASN A:708 , ALA A:711 , TYR A:714 , ASN A:718 , GLY A:720 , ASN A:721 , LEU A:722 , GLY A:723 , PHE A:732 , HIS A:733 , GLC A:822 , HOH A:902 , HOH A:924 , HOH A:928 , HOH A:931 , HOH A:933 , HOH A:1009 , HOH A:1070binding site for Poly-Saccharide residues GLC A 826 through GLC A 832
09AC9SOFTWAREASP 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 , 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:826 , HOH A:902 , HOH A:928 , HOH A:933 , HOH A:969 , HOH A:1009 , HOH A:1021 , HOH A:1165 , HOH A:1323binding site for Poly-Saccharide residues GLC A 833 through GLC A 836
10AD1SOFTWAREGLY A:138 , ASN A:534 , THR A:537 , PHE A:538 , MET A:540 , ASP A:571 , TRP A:573 , GLN A:574 , TRP A:655 , PRO A:687 , PRO A:689 , SER A:717 , MET A:719 , GLC A:833 , HOH A:969 , HOH A:1021 , HOH A:1106 , HOH A:1323binding site for Poly-Saccharide residues GLC A 837 through GLC A 839

(-) SS Bonds  (0, 0)

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

(-) 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 5GQX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GQX)

(-) 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.....eeeeee....eeee.ee.....eeeeeee.......eeeeee..eeeee...........hhhhhhhhhh....hhhhh.eeeeeee..eeeeeeeee.....eeeeee.hhh........eee...eeeeeee......eeeeeee.....eeee...............ee...........hhhhhhhhhh.hhhhh..eeeee......eee....eee..eee...........eee.hhhhhhhhhhhhhhhhh..eeee...ee..hhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh..eeeeee....ee..................hhhhhee....ee.....hhhhhhhhhhhhhhhhhhhh..eeee..hhhhhh...................hhhhhhhhhhhhhhhhhhh...eeee...........hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhh......hhhhh..hhhhhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh.eeeee.......eeeeee...hhhhheeeeee.....eeeeeeee....eeeeeee..hhhhh........eee..........eeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gqx A   5 ISADQVNQIIYNLHHDPFEILGCHLLEEGKNTKKWVVRAYLPKAEAAWVIRPTERKEDPMNSVHHPNFFECIIETPELNHYQLKVKEGEHEKVIYDPYAFSSPYLTDEDIYLFSEGNHHRIYEKLGAHVGEINGVKGVYFAVWAPNARNVSVIGDFNNWDGREHQMRKRNYTIWELFVPEIGSGTVYKYEIKNSEGHIYEKSDPYGFYREVRPNTASIVVDIDNIYQWHDEEWLEKRRNSDPLKQPVSVYEVHLGSWLHGSSAEKMPLLNGEADPVIVSEWNPGARFLSYYELAEKLIPYVKDMGYTHIELLPIAEHPFDGSWGYQVTGFYSPTSRFGRPEDFMYFVDKCHENGIGVILDWVPGHFPKDSHGLAYFDGTHLYEHADPRIGEHKEWGTLVFNYGRHEVRNFLVANVLFWFDKYHVDGIRVDAVASMLYRNYLRKEGEWIANEYGGDEHIEAVSFIREVNTLLFEYFPGILSIAEESTEWEKVSRPVYDGGLGFNLKWDMGWMHDMLDYFNIDPYFRQYHQNNVTFSMLYYYNENFMLALSHDEIVHGKSNMLGKMPGDEWQKYANVRALFTYMYTHPGKKTMFMSMEFGQWSEWNVNGDLEWHLLQYEPHQQLKQFFTDLNALYQQEPALYTHDFEYHGFEWIDCNDNTHSVVSFLRRSDDPNDSLVVVCNFTPQPHSHYRIGVPEAGYYVELFNSDAKQYGGSNMGNLGGKWADEWSFHNKPYSLDLCLPPLAVLILKLDPTKVP 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 5GQX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5gqv 5gqw

(-) Related Entries Specified in the PDB File

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