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(-) Description

Title :  GGGPS FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS
 
Authors :  C. Rajendran, D. Peterhoff, B. Beer, E. P. Kumpula, E. Kapetaniou, H. Gu R. K. Wierenga, R. Sterner, P. Babinger
Date :  07 Sep 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,E  (1x)
Biol. Unit 4:  D,F  (1x)
Keywords :  Gggps, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Peterhoff, B. Beer, C. Rajendran, E. P. Kumpula, E. Kapetaniou, H. Guldan, R. K. Wierenga, R. Sterner, P. Babinger
A Comprehensive Analysis Of The Geranylgeranylglyceryl Phosphate Synthase Enzyme Family Identifies Novel Members And Reveals Mechanisms Of Substrate Specificity And Quaternary Structure Organization.
Mol. Microbiol. V. 92 885 2014
PubMed-ID: 24684232  |  Reference-DOI: 10.1111/MMI.12596

(-) Compounds

Molecule 1 - GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE
    Chains: A, B, C, D, E, F
    EC Number: 2.5.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MTH_552
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS STR. DELTA H
    Organism Taxid: 187420
    Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H
    Synonym: GGGP SYNTHASE, GGGPS, MTGGGPS, (S)-3-O- GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE, PHOSPHOGLYCEROL GERANYLGERANYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x): AB    
Biological Unit 3 (1x):   C E 
Biological Unit 4 (1x):    D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
11GP6Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2PGE6Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
11GP6Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2PGE6Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
11GP2Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
11GP2Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
11GP2Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:23 , TYR A:172 , GLU A:174 , SER A:177 , GLY A:178 , GLY A:202 , GLY A:203 , GLY A:204 , GLY A:225 , THR A:226 , HOH A:414BINDING SITE FOR RESIDUE 1GP A 301
02AC2SOFTWAREPRO A:80 , PHE A:95 , TRP A:106BINDING SITE FOR RESIDUE PGE A 302
03AC3SOFTWARELEU B:23 , TYR B:172 , GLU B:174 , SER B:177 , GLY B:178 , GLY B:202 , GLY B:203 , GLY B:204 , GLY B:225BINDING SITE FOR RESIDUE 1GP B 301
04AC4SOFTWAREVAL B:86 , TRP B:106 , GLN B:111 , GLY B:114BINDING SITE FOR RESIDUE PGE B 302
05AC5SOFTWARELEU C:23 , TYR C:172 , GLU C:174 , SER C:177 , GLY C:178 , GLY C:202 , GLY C:203 , GLY C:204 , GLY C:225 , THR C:226BINDING SITE FOR RESIDUE 1GP C 301
06AC6SOFTWAREPRO C:80 , GLY C:81 , LEU C:98 , GLN C:111BINDING SITE FOR RESIDUE PGE C 302
07AC7SOFTWARELEU D:23 , PHE D:79 , TYR D:172 , GLU D:174 , SER D:177 , GLY D:178 , GLY D:202 , GLY D:203 , GLY D:204 , THR D:224 , GLY D:225BINDING SITE FOR RESIDUE 1GP D 301
08AC8SOFTWAREPRO D:80 , LEU D:98 , GLN D:111BINDING SITE FOR RESIDUE PGE D 302
09AC9SOFTWARELEU E:23 , PHE E:79 , TYR E:172 , GLU E:174 , SER E:177 , GLY E:178 , GLY E:202 , GLY E:203 , GLY E:204 , GLY E:225BINDING SITE FOR RESIDUE 1GP E 301
10BC1SOFTWAREVAL E:86 , PHE E:95 , ALA E:110BINDING SITE FOR RESIDUE PGE E 302
11BC2SOFTWARELEU F:23 , TYR F:172 , GLU F:174 , SER F:177 , GLY F:178 , GLY F:202 , GLY F:203 , GLY F:204 , THR F:224BINDING SITE FOR RESIDUE 1GP F 301
12BC3SOFTWAREPRO F:80 , GLY F:81 , ASN F:82 , VAL F:86 , TRP F:106 , GLN F:111 , GLY F:114BINDING SITE FOR RESIDUE PGE F 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MM1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:134 -Pro A:135
2Glu B:134 -Pro B:135
3Glu D:134 -Pro D:135
4Glu E:134 -Pro E:135
5Lys F:3 -Met F:4
6Ala F:65 -Arg F:66
7Arg F:69 -Glu F:70
8Glu F:134 -Pro F:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MM1)

(-) Exons   (0, 0)

(no "Exon" information available for 4MM1)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeee..hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm1 A   2 FKMKVEDYFHDILRERKIHLTLIDPEEQTPEEAVEIARAAIRGGTDGIMLGGSTTDSSELDNTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVTGTVEDKIREIVEGMG 246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     ||238        
                                                                                                                                                                                                                                                           227|           
                                                                                                                                                                                                                                                            235           


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...eeeeeehhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeee..hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee............hhhhhhhhh..eeee.....hhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm1 B   5 KVEDYFHDILRERKIHLTLIDPEEQTPEEAVEIAGTDGIMLGGSTTDSSELDNTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVTG 225
                                    14        24        34   ||   50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
                                                            38|                                                                                                                                                                                    
                                                             45                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeeeee...................eeee......hhhhhhhhhhhhhh...eeee..hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mm1 C   1 MFKMKVEDYFHDILRERKIHLTLIDPEEQTPIARAAIRGGTDGIMLGGSTTDSSELDNTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVTGTDKIREIVEGMGSV 248
                                    10        20        30||      45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225||     244    
                                                         31|                                                                                                                                                                                          226|            
                                                          37                                                                                                                                                                                           236            


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....eeeeehhhhh.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh...eeee..hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm1 D   2 FKMKVEDYFHDILRERKIHLTLIDPEEQAVEIARAAIRGGTDGIMLGGSTTDSSELDNTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVTG 225
                                    11        21       |35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                      29|                                                                                                                                                                                               
                                                       34                                                                                                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh...eeee..hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm1 E   1 MFKMKVEDYFHDILRERKIHLTLIDPEEQTPEEAVEIARAAIRGGTDGIMLGGSTTDSSELDNTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVTG 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     


Chain F from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeeee...hhhhhhhhhhh....eee..............eee...hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh........hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm1 F   2 FKMKVEDYFHDILRERKIHLTLIDPEAVEIARAAIRGGTDGIMLGGTARALRENIDVPIILFPGNTTGVSRYADAIFFMSLLNSTNPYWIIGAQALGAATVKKMGIEALPMGYLVVEPGGTVGWVGDTKPVPRNKPDIAAAYAMAAEFLGMRLFYLEAGSGAPEHVPEEMIALVKRCTDQILIVGGGIRSGEDAARVAGAGADVVVT 224
                                    11        21    ||  37        47     || 67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
                                                   26|                  53|                                                                                                                                                                
                                                    33                   64
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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 4MM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MM1)

(-) Gene Ontology  (10, 10)

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