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(-) Description

Title :  2.95A RESOLUTION STRUCTURE OF APO INDEPENDENT PHOSPHOGLYCERATE MUTASE FROM C. ELEGANS (MONOCLINIC 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 :  2.95
Chains :  Asym./Biol. Unit :  A,B
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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MN2Ligand/IonMANGANESE (II) ION
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , ASN A:336binding site for residue CL A 601
2AC2SOFTWAREARG A:216 , ARG A:284binding site for residue CL A 602
3AC3SOFTWAREASP A:426 , HIS A:430 , HIS A:485binding site for residue MN A 603
4AC4SOFTWAREASP A:37 , SER A:86 , LYS A:359 , ASP A:467 , HIS A:468binding site for residue ZN A 604
5AC5SOFTWAREARG B:97 , ASN B:336binding site for residue CL B 601
6AC6SOFTWAREARG B:216 , ARG B:284binding site for residue CL B 602
7AC7SOFTWAREASP B:426 , HIS B:430 , HIS B:485binding site for residue MN B 603
8AC8SOFTWAREASP B:37 , SER B:86 , LYS B:359 , ASP B:467 , HIS B:468binding site for residue ZN B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KGM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KGM)

(-) 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:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeeeee...........hhhhhh.hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhh......eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee.......................eeee.....eee........hhhhhhhhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgm A  20 AMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLETTGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKI 539
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      |200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530         
                                                                                                                                                                                                          196|                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                           198                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.........hhhhhh.hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhh.....eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee..hhhhh.....eeee.......hhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee.hhh.................eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee....................eeee.....eee........hhhhhhhhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgm B  20 AMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLETGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKI 539
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      |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       471       481       491       501       511       521       531        
                                                                                                                                                                                                          196|                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                           199
   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 5KGM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        GPMI_CAEEL | G5EFZ1: 5kgl 5kgn

(-) Related Entries Specified in the PDB File

5kgl 5kgn