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(-) Description

Title :  2.45A RESOLUTION STRUCTURE OF APO INDEPENDENT PHOSPHOGLYCERATE MUTASE FROM C. ELEGANS (ORTHORHOMBIC FORM)
 
Authors :  S. Lovell, N. Mehzabeen, K. P. Battaile, H. Yu, P. Dranchak, R. Macarthu T. Carlow, H. Suga, J. Inglese
Date :  13 Jun 16  (Deposition) - 05 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metal Binding, Coupled Enzyme Assay, Hts, Structure Activity Relationship, Rapid Systems, High Throughput Enzymology, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yu, P. Dranchak, Z. Li, R. Macarthur, M. S. Munson, N. Mehzabeen, N. J. Baird, K. P. Battalie, D. Ross, S. Lovell, C. K. Carlow, H. Suga, J. Inglese
Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases.
Nat Commun V. 8 14932 2017
PubMed-ID: 28368002  |  Reference-DOI: 10.1038/NCOMMS14932

(-) Compounds

Molecule 1 - 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
    Chains: A, B
    EC Number: 5.4.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: C2566/T7 EXPRESS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ISOFORM A
    Gene: IPGM-1, F57B10.3
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Other Details: FULL LENGTH (M1 TO I539, ISOFORM A)
    Synonym: IPGM,COFACTOR-INDEPENDENT PHOSPHOGLYCERATE MUTASE HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MN2Ligand/IonMANGANESE (II) ION
3SO47Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:212 , LYS B:306binding site for residue CL A 601
02AC2SOFTWAREASP A:426 , HIS A:430 , HIS A:485binding site for residue MN A 602
03AC3SOFTWAREASP A:37 , SER A:86 , LYS A:359 , ASP A:467 , HIS A:468binding site for residue ZN A 603
04AC4SOFTWAREARG A:105 , PHE A:331 , HOH A:706binding site for residue SO4 A 604
05AC5SOFTWAREHIS A:147 , ARG A:177 , ARG A:216 , ARG A:284 , ARG A:287 , HOH A:707binding site for residue SO4 A 605
06AC6SOFTWAREARG A:97 , ALA A:334 , SER A:335 , ASN A:336 , LYS A:337 , HOH A:710binding site for residue SO4 A 606
07AC7SOFTWARELYS A:306 , TYR B:212binding site for residue CL B 601
08AC8SOFTWAREASP B:426 , HIS B:430 , HIS B:485binding site for residue MN B 602
09AC9SOFTWAREASP B:37 , SER B:86 , ASP B:467 , HIS B:468binding site for residue ZN B 603
10AD1SOFTWAREHIS B:147 , ARG B:177 , ARG B:216 , ARG B:284 , ARG B:287binding site for residue SO4 B 604
11AD2SOFTWAREARG B:105 , PHE B:331binding site for residue SO4 B 605
12AD3SOFTWAREARG B:177 , ASP B:217 , ARG B:222 , ARG B:287binding site for residue SO4 B 606
13AD4SOFTWAREARG B:97 , ALA B:334 , SER B:335 , ASN B:336 , LYS B:337binding site for residue SO4 B 607

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:532 -Val A:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KGL)

(-) 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:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...eeeeee..................hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhh....eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......................eeee.....eee........hhhhhhhhhhhhh.............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgl A  20 AMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLEKTTGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKI 539
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539


Chain B from PDB  Type:PROTEIN  Length:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeeeee...........hhhhhh.hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh.....eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee.hhhhhh.....eeee....hhhhhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee.hhh.................eeeeee..............hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee.......................eeee.....eee........hhhhhhhhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgl B  20 AMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLEKTTGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKI 539
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539
   Legend:   → Mismatch (orange background)
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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 5KGL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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        GPMI_CAEEL | G5EFZ1: 5kgm 5kgn

(-) Related Entries Specified in the PDB File

5kgm 5kgn