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(-) Description

Title :  STRUCTURE OF THE H477R VARIANT OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE AND GTP.
 
Authors :  T. Holyoak, D. S. Cui
Date :  23 Mar 17  (Deposition) - 12 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphoenolpyruvate Carboxykinase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Cui, A. Broom, M. J. Mcleod, E. M. Meiering, T. Holyoak
Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening And Closing In Cytosolic Phosphoenolpyruvate Carboxykinase.
Biochemistry V. 56 2106 2017
PubMed-ID: 28345895  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00178

(-) 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  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION
4OXL1Ligand/IonOXALATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , GTP A:703 , OXL A:704binding site for residue MN A 701
2AC2SOFTWARETHR A:291 , ASP A:310 , GTP A:703 , HOH A:813 , HOH A:814 , HOH A:825binding site for residue MN A 702
3AC3SOFTWAREHIS 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 , PRO A:337 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , PHE A:530 , ASN A:533 , MN A:701 , MN A:702 , OXL A:704 , HOH A:813 , HOH A:814 , HOH A:848 , HOH A:849 , HOH A:909 , HOH A:923 , HOH A:964 , HOH A:1011 , HOH A:1056 , HOH A:1069binding site for residue GTP A 703
4AC4SOFTWAREARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , ARG A:405 , ALA A:467 , MN A:701 , GTP A:703 , HOH A:829 , HOH A:834 , HOH A:955binding site for residue OXL A 704
5AC5SOFTWARELEU A:79 , ASN A:208 , HOH A:918 , HOH A:970 , HOH A:1083binding site for residue NA A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V9G)

(-) 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 5V9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V9G)

(-) Exons   (0, 0)

(no "Exon" information available for 5V9G)

(-) 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:620
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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...hhhhhh..hhhhhhhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee...........eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhhh...eeee..eeee.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v9g A   3 PQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMRDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622
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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 5V9G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V9G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V9G)

(-) 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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  5v9g
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  4.1.1.32
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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 5fh4 5fh5 5v95 5v97 5v9f 5v9h

(-) Related Entries Specified in the PDB File

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5v97 SAME ENZYME VARIANT WITH DIFFERENT LIGATION STATE
5v9f SAME ENZYME VARIANT WITH DIFFERENT LIGATION STATE
5v9h