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(-) Description

Title :  THE STRUCTURE OF RAT CYTOSOLIC PEPCK VARIANT E89D IN COMPLEX WITH BETA-SULFOPYRUVATE AND GTP
 
Authors :  T. A. Johnson, T. Holyoak
Date :  21 Dec 15  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
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]
    Chains: A
    EC Number: 4.1.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCK1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PEPCK-C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MN3Ligand/IonMANGANESE (II) ION
4NA1Ligand/IonSODIUM ION
5SPV1Ligand/IonSULFOPYRUVATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:291 , GTP A:704 , HOH A:817 , HOH A:837 , HOH A:970binding site for residue MN A 701
2AC2SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , GTP A:704 , SPV A:705binding site for residue MN A 702
3AC3SOFTWAREHIS A:502 , GLU A:607 , HOH A:891 , HOH A:1193binding site for residue MN A 703
4AC4SOFTWAREHIS A:264 , PRO A:285 , SER A:286 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ASP A:311 , VAL A:335 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:701 , MN A:702 , SPV A:705 , HOH A:803 , HOH A:817 , HOH A:837 , HOH A:853 , HOH A:865 , HOH A:869 , HOH A:889 , HOH A:893 , HOH A:895 , HOH A:994 , HOH A:1055binding site for residue GTP A 704
5AC5SOFTWAREARG A:87 , GLY A:237 , LYS A:243 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , ARG A:405 , MN A:702 , GTP A:704 , HOH A:878 , HOH A:1002 , HOH A:1126binding site for residue SPV A 705
6AC6SOFTWAREARG A:543 , TYR A:557 , HOH A:913 , HOH A:1080binding site for residue EDO A 706
7AC7SOFTWAREGLU A:274 , ARG A:437 , ILE A:475 , HOH A:822binding site for residue EDO A 707
8AC8SOFTWARELEU A:79 , ASN A:208 , HOH A:1084 , HOH A:1115 , HOH A:1238binding site for residue NA A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FH4)

(-) 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 5FH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FH4)

(-) Exons   (0, 0)

(no "Exon" information available for 5FH4)

(-) 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:612
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...ee.......eee.........hhh.eeee..hhhhh.............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeeehhh.eeeee...hhhhhh.......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.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fh4 A   4 QLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIDSKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEAGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463||     480       490       500       510       520       530       540       550       560       570       580       590       600       610       620  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      464|                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       472
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  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 5FH4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FH4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FH4)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:200 - Pro A:201   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCKGC_RAT | P07379: 2qew 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 5fh5 5v95 5v97 5v9f 5v9g 5v9h

(-) Related Entries Specified in the PDB File

5fh0 5fh1 5fh2 5fh3 5fh5