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(-) Description

Title :  STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH BETA-SULFOPYRUVATE AND GTP
 
Authors :  T. A. Johnson, T. Holyoak
Date :  17 Aug 12  (Deposition) - 03 Jul 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Gluconeogenesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Johnson, T. Holyoak
The {Omega}-Loop Lid Domain Of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function.
Biochemistry V. 51 9547 2012
PubMed-ID: 23127136  |  Reference-DOI: 10.1021/BI301278T

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
    Chains: A
    EC Number: 4.1.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: PCK1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PEPCK-C, PHOSPHOENOLPYRUVATE CARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MN2Ligand/IonMANGANESE (II) ION
4NA1Ligand/IonSODIUM ION
5SPV1Ligand/IonSULFOPYRUVATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS 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:702 , MN A:703 , SPV A:705 , HOH A:817 , HOH A:832 , HOH A:838 , HOH A:852 , HOH A:857 , HOH A:907 , HOH A:925 , HOH A:1019 , HOH A:1102 , HOH A:1131 , HOH A:1231 , HOH A:1247BINDING SITE FOR RESIDUE GTP A 701
2AC2SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , GTP A:701 , SPV A:705BINDING SITE FOR RESIDUE MN A 702
3AC3SOFTWARETHR A:291 , GTP A:701 , HOH A:822 , HOH A:852 , HOH A:857BINDING SITE FOR RESIDUE MN A 703
4AC4SOFTWARELEU A:79 , ASN A:208 , HOH A:959 , HOH A:987 , HOH A:1093BINDING SITE FOR RESIDUE NA A 704
5AC5SOFTWAREARG A:87 , GLY A:237 , LYS A:243 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , PHE A:333 , ARG A:405 , GTP A:701 , MN A:702 , HOH A:802 , HOH A:825 , HOH A:868BINDING SITE FOR RESIDUE SPV A 705
6AC6SOFTWAREALA A:128BINDING SITE FOR RESIDUE 1PE A 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GNO)

(-) 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 4GNO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GNO)

(-) Exons   (0, 0)

(no "Exon" information available for 4GNO)

(-) 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:613
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4gnoa1 A:2-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                     d4gnoa2 A:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...ee.......eee.........hhh.eeee..hhhhhh............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.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gno A   2 PPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEGGGIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461    || 479       489       499       509       519       529       539       549       559       569       579       589       599       609       619   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          466|                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           475
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GNO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GNO)

(-) 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 4gnp 4gnq 4ox2 4yw8 4yw9 4ywb 4ywd 5fh0 5fh1 5fh2 5fh3 5fh4 5fh5 5v95 5v97 5v9f 5v9g 5v9h

(-) Related Entries Specified in the PDB File

4gmm STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH SULFOPYRUVATE AND GTP
4gmu STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH OXALATE AND GTP
4gmw STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH PEP AND GDP
4gmz STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH SULFOPYRUVATE AND GTP
4gnl STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH PEP AND GDP
4gnm STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH OXALATE AND GTP
4gnp STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH PEP AND GDP
4gnq STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH OXALATE AND GTP