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(-) Description

Title :  CRYSTAL STRUCTURE OH HUMAN PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5 (PGAM5)
 
Authors :  A. Chaikuad, I. Alfano, S. Picaud, P. Filippakopoulos, A. Barr, F. Von C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, K. Takeda, H. I S. Knapp, Structural Genomics Consortium (Sgc)
Date :  07 May 10  (Deposition) - 15 Sep 10  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Pgam5, Phosphoglycerate Mutase Family Member 5, Bxlbv68, Mgc5352 Protein, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, P. Filippakopoulos, S. R. Marcsisin, S. Picaud, M. Schroder, S. Sekine, H. Ichijo, J. R. Engen, K. Takeda, S. Knapp
Structures Of Pgam5 Provide Insight Into Active Site Plasticity And Multimeric Assembly.
Structure 2017
PubMed-ID: 28648608  |  Reference-DOI: 10.1016/J.STR.2017.05.020

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN PHOSPHATASE PGAM5, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 90-289
    Gene: PGAM5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5, BCL-XL-BINDING PROTEIN V68

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREEDO A:8 , HIS A:261 , ARG A:273 , THR A:274 , HOH A:310 , ASN B:255BINDING SITE FOR RESIDUE EDO A 6
02AC2SOFTWAREEDO A:6 , ARG A:134 , ASP A:277 , HOH A:297BINDING SITE FOR RESIDUE EDO A 8
03AC3SOFTWARETHR A:157 , ASP A:158 , LYS A:169 , HOH A:300 , HOH A:370BINDING SITE FOR RESIDUE EDO A 10
04AC4SOFTWAREARG A:104 , ALA A:231 , ARG A:235 , SER A:253 , LEU A:254 , ARG A:288BINDING SITE FOR RESIDUE EDO A 11
05AC5SOFTWAREGLY A:279 , PHE A:280 , MET A:281 , PRO A:282 , HOH A:371 , HOH B:6 , EDO B:7 , ARG B:134BINDING SITE FOR RESIDUE EDO A 12
06AC6SOFTWAREALA A:206 , HOH A:324 , GLU B:205 , ARG B:240BINDING SITE FOR RESIDUE EDO A 13
07AC7SOFTWAREMET A:89 , ASP A:90 , ARG A:209 , ARG A:240 , HOH A:318 , ASN B:210BINDING SITE FOR RESIDUE EDO A 16
08AC8SOFTWAREHIS A:99 , HIS A:261 , VAL A:263 , ARG A:265 , ALA A:271 , ARG A:273 , HOH A:336 , GLU B:220 , ARG B:288 , HOH B:388 , HOH B:421BINDING SITE FOR RESIDUE PG4 A 1
09AC9SOFTWARESER A:148 , ARG A:152BINDING SITE FOR RESIDUE CL A 2
10BC1SOFTWAREHOH A:324 , CYS B:239 , ARG B:240 , PHE B:244 , PRO B:245 , PRO B:246 , GLY B:248 , TRP B:249 , HOH B:298BINDING SITE FOR RESIDUE EDO B 1
11BC2SOFTWAREHOH B:80 , HIS B:147 , THR B:157 , ASP B:158 , LYS B:169BINDING SITE FOR RESIDUE EDO B 3
12BC3SOFTWAREHIS B:91 , TYR B:92 , LYS B:93 , HIS B:213 , ALA B:215BINDING SITE FOR RESIDUE EDO B 4
13BC4SOFTWAREPGE B:2 , EDO B:17 , HOH B:71 , ARG B:134 , ASP B:277BINDING SITE FOR RESIDUE EDO B 5
14BC5SOFTWAREEDO A:12 , HOH A:35 , ARG A:134 , GLY B:279 , HOH B:296BINDING SITE FOR RESIDUE EDO B 7
15BC6SOFTWAREGLN B:107 , TYR B:108 , HIS B:109 , VAL B:110 , ASP B:222 , SER B:289 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE EDO B 15
16BC7SOFTWAREASN A:255 , PGE B:2 , EDO B:5 , HOH B:71 , HIS B:261 , ARG B:273 , THR B:274BINDING SITE FOR RESIDUE EDO B 17
17BC8SOFTWAREHOH B:61 , LYS B:93 , ALA B:215 , ALA B:217 , HOH B:327BINDING SITE FOR RESIDUE EDO B 18
18BC9SOFTWAREHOH A:341 , EDO B:5 , EDO B:17 , HIS B:99 , LEU B:140 , TYR B:224 , HIS B:261 , ARG B:273 , HOH B:389 , HOH B:420BINDING SITE FOR RESIDUE PGE B 2
19CC1SOFTWAREHOH A:86 , MET B:89 , ASP B:90 , HIS B:91 , HIS B:213 , ARG B:240 , HOH B:340 , HOH B:355 , HOH B:385BINDING SITE FOR RESIDUE PEG B 290
20CC2SOFTWARESER B:148 , ARG B:152BINDING SITE FOR RESIDUE CL B 291

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MXO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MXO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MXO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MXO)

(-) Exons   (0, 0)

(no "Exon" information available for 3MXO)

(-) 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:188
 aligned with PGAM5_HUMAN | Q96HS1 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:202
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287  
          PGAM5_HUMAN    88 KLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee.........hhhhh..hhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh.....eeeehhhh....--------------.hhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhh..hhhhhhhh......eeeeee.....eeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxo A  88 SMDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAP--------------VQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
                                    97       107       117       127       137       147       157       167       177  |      -       197       207       217       227       237       247       257       267       277       287  
                                                                                                                      180            195                                                                                              


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with PGAM5_HUMAN | Q96HS1 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:202
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287  
          PGAM5_HUMAN    88 KLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------His_Phos_1-3mxoB01 B:99-237                                                                                                                ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------His_Phos_1-3mxoB02 B:99-237                                                                                                                ---------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........eeeeeee.........hhhhh..hhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh.....eeeehhhh...-----------hhhhhhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhh....hhhhhh......eeeeee.....eeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxo B  88 SMDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGA-----------KPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
                                    97       107       117       127       137       147       157       167       177 |       -   |   197       207       217       227       237       247       257       267       277       287  
                                                                                                                     179         191
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3MXO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MXO)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PGAM5_HUMAN | Q96HS1)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0009400    signal transducer, downstream of receptor, with serine/threonine phosphatase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0070266    necroptotic process    A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PGAM5_HUMAN | Q96HS1: 3o0t 5muf

(-) Related Entries Specified in the PDB File

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