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(-) Description

Title :  THE STRUCTURE OF RAT CYTOSOLIC PEPCK VARIANT E89Q IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP
 
Authors :  T. A. Johnson, T. Holyoak
Date :  21 Dec 15  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Gluconeogenesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Johnson, M. J. Mcleod, T. Holyoak
Utilization Of Substrate Intrinsic Binding Energy For Conformational Change And Catalytic Function In Phosphoenolpyruvate Carboxykinase.
Biochemistry V. 55 575 2016
PubMed-ID: 26709450  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01215

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
    ChainsA
    EC Number4.1.1.32
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePCK1
    MutationYES
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPEPCK-C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION
4PGA1Ligand/Ion2-PHOSPHOGLYCOLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:291 , GDP A:703 , HOH A:807 , HOH A:815 , HOH A:886 , HOH A:994binding site for residue MN A 701
2AC2SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , PGA A:704 , HOH A:819 , HOH A:920binding site for residue MN A 702
3AC3SOFTWAREPRO A:285 , SER A:286 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , PRO A:528 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:701 , HOH A:807 , HOH A:815 , HOH A:826 , HOH A:838 , HOH A:841 , HOH A:854 , HOH A:857 , HOH A:899 , HOH A:994 , HOH A:1123binding site for residue GDP A 703
4AC4SOFTWAREARG A:87 , GLY A:236 , GLY A:237 , LYS A:244 , ASP A:311 , ARG A:405 , MN A:702 , HOH A:815 , HOH A:819 , HOH A:832 , HOH A:837 , HOH A:920 , HOH A:973binding site for residue PGA A 704
5AC5SOFTWARELEU A:79 , ASN A:208 , HOH A:869 , HOH A:965 , HOH A:1199binding site for residue NA A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FH5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FH5)

(-) Exons   (0, 0)

(no "Exon" information available for 5FH5)

(-) 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    
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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:610
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eee.....eeee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeeehhh.eeeee...hhhhh........hhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee....eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fh5 A   6 HNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIQSKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465|      482       492       502       512       522       532       542       552       562       572       582       592       602       612       622
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     465|                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      473                                                                                                                                                     

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  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 5FH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FH5)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCKGC_RAT | P073792qew 2qey 2qf1 2qf2 2rk7 2rk8 2rka 2rkd 2rke 3dt2 3dt4 3dt7 3dtb 3moe 3mof 3moh 4gmm 4gmu 4gmw 4gmz 4gnl 4gnm 4gno 4gnp 4gnq 4ox2 4yw8 4yw9 4ywb 4ywd 5fh0 5fh1 5fh2 5fh3 5fh4 5v95 5v97 5v9f 5v9g 5v9h

(-) Related Entries Specified in the PDB File

5fh0 5fh1 5fh2 5fh3 5fh4