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(-) Description

Title :  STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 3-MERCAPTOPICOLINIC ACID AND OXALIC ACID
 
Authors :  M. D. Balan, T. A. Johnson, W. R. Lotosky, M. J. Mcleod, T. Holyoak
Date :  20 Mar 15  (Deposition) - 23 Sep 15  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Kinase, Gluconeogenesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Balan, M. J. Mcleod, W. R. Lotosky, M. Ghaly, T. Holyoak
Inhibition And Allosteric Regulation Of Monomeric Phosphoenolpyruvate Carboxykinase By 3-Mercaptopicolinic Acid.
Biochemistry V. 54 5878 2015
PubMed-ID: 26322521  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00822

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
    Chains: A, C
    EC Number: 4.1.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: PCK1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PEPCK-C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
11WD2Ligand/Ion3-SULFANYLPYRIDINE-2-CARBOXYLIC ACID
2CL2Ligand/IonCHLORIDE ION
3MN4Ligand/IonMANGANESE (II) ION
4NA2Ligand/IonSODIUM ION
5OXD2Ligand/IonOXALIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
11WD1Ligand/Ion3-SULFANYLPYRIDINE-2-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
4NA-1Ligand/IonSODIUM ION
5OXD1Ligand/IonOXALIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
11WD1Ligand/Ion3-SULFANYLPYRIDINE-2-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
4NA-1Ligand/IonSODIUM ION
5OXD1Ligand/IonOXALIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , OXD A:704 , HOH A:1086binding site for residue MN A 701
02AC2SOFTWAREHIS A:502 , GLU A:607 , HOH A:947 , HOH A:1134 , HOH A:1280binding site for residue MN A 702
03AC3SOFTWARELEU A:79 , ASN A:208 , HOH A:999 , HOH A:1062 , HOH A:1304binding site for residue NA A 703
04AC4SOFTWAREARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , ARG A:405 , MN A:701 , HOH A:923 , HOH A:1063 , HOH A:1086 , HOH A:1099binding site for residue OXD A 704
05AC5SOFTWAREPHE A:284 , CYS A:288 , GLY A:434 , GLY A:435 , ARG A:436 , VAL A:514 , ASN A:515 , TRP A:516 , PHE A:517binding site for residue 1WD A 705
06AC6SOFTWARETYR A:235 , GLY A:237 , ASN A:403binding site for residue CL A 706
07AC7SOFTWARELYS C:244 , HIS C:264 , ASP C:311 , OXD C:704 , HOH C:1140binding site for residue MN C 701
08AC8SOFTWAREHIS C:502 , GLU C:607 , HOH C:843 , HOH C:1155 , HOH C:1269binding site for residue MN C 702
09AC9SOFTWARELEU C:79 , ASN C:208 , HOH C:1050 , HOH C:1087 , HOH C:1306binding site for residue NA C 703
10AD1SOFTWAREARG C:87 , LYS C:244 , HIS C:264 , SER C:286 , ASP C:311 , ARG C:405 , MN C:701 , HOH C:935 , HOH C:997 , HOH C:1103 , HOH C:1140binding site for residue OXD C 704
11AD2SOFTWARECYS C:288 , GLY C:434 , GLY C:435 , ARG C:436 , VAL C:514 , ASN C:515 , TRP C:516 , PHE C:517 , HOH C:1192binding site for residue 1WD C 705
12AD3SOFTWARETYR C:235 , GLY C:237 , ASN C:403 , HOH C:997binding site for residue CL C 706

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:288 -A:705
2C:288 -C:705

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:200 -Pro A:201
2Leu C:200 -Pro C:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YWB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YWB)

(-) Sequences/Alignments

Asymmetric 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...eee.....eeee.........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..............hhhhhhhhhhhhhhhhhh...eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ywb A   3 PQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 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||     405       415       425       435       445       455       465||     480       490       500       510       520       530       540       550       560       570       580       590       600       610       620  
                                                                                                                                                                                                                                                                                                                                                                                                                                393|                                                                  466|                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                 397                                                                   472                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ywb C   9 LDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388    || 399       409       419       429       439       449       459     ||476       486       496       506       516       526       536       546       556       566       576       586       596       606       616      
                                                                                                                                                                                                                                                                                                                                                                                                                          393|                                                                   465|                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                           395                                                                    473
   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  (0, 0)

(no "SCOP Domain" information available for 4YWB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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        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 4ywd 5fh0 5fh1 5fh2 5fh3 5fh4 5fh5 5v95 5v97 5v9f 5v9g 5v9h

(-) Related Entries Specified in the PDB File

4yw8 4yw9