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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE FROM COCCIDIOIDES IMMITIS SOLVED BY COMBINED SAD MR
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  16 Nov 10  (Deposition) - 15 Dec 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Coccidioidomycosis, Coccidioides, Valley Fever, Immitis, Posadasii, Fructose-1, 6-Bisphosphate Aldolase, Zinc- Containing Enzyme, Pathogenic Fungus, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J Struct Funct Genomics V. 12 83 2011
PubMed-ID: 21359836  |  Reference-DOI: 10.1007/S10969-011-9101-7

(-) Compounds

Molecule 1 - PUTATIVE FRUCTOSE-BISPHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: CIMG_05755
    Organism Common: VALLEY FEVER FUNGUS
    Organism Scientific: COCCIDIOIDES IMMITIS
    Organism Taxid: 5501
    Synonym: FBP ALDOLASE, FBPA, PUTATIVE FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 35)

Asymmetric/Biological Unit (2, 35)
No.NameCountTypeFull Name
1IOD33Ligand/IonIODIDE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR B:20BINDING SITE FOR RESIDUE IOD B 304
02AC2SOFTWARETRP B:57 , HOH B:339BINDING SITE FOR RESIDUE IOD B 306
03AC3SOFTWAREGLN B:89BINDING SITE FOR RESIDUE IOD B 307
04AC4SOFTWAREARG B:96BINDING SITE FOR RESIDUE IOD B 308
05AC5SOFTWARELYS B:95 , HOH B:357BINDING SITE FOR RESIDUE IOD B 309
06AC6SOFTWAREGLN A:89BINDING SITE FOR RESIDUE IOD A 303
07AC7SOFTWAREILE A:93BINDING SITE FOR RESIDUE IOD A 304
08AC8SOFTWAREARG A:96BINDING SITE FOR RESIDUE IOD A 305
09AC9SOFTWARELYS A:95 , GLU A:131 , IOD A:307BINDING SITE FOR RESIDUE IOD A 306
10BC1SOFTWAREGLU A:131 , IOD A:306BINDING SITE FOR RESIDUE IOD A 307
11BC2SOFTWAREARG A:239BINDING SITE FOR RESIDUE IOD A 309
12BC3SOFTWARETYR A:204BINDING SITE FOR RESIDUE IOD A 310
13BC4SOFTWARETYR A:195BINDING SITE FOR RESIDUE IOD A 311
14BC5SOFTWARELYS A:261BINDING SITE FOR RESIDUE IOD A 314
15BC6SOFTWAREHIS A:21BINDING SITE FOR RESIDUE IOD A 315
16BC7SOFTWAREHOH A:458BINDING SITE FOR RESIDUE IOD A 316
17BC8SOFTWAREASN B:252 , HOH B:370BINDING SITE FOR RESIDUE IOD B 311
18BC9SOFTWAREASN A:194BINDING SITE FOR RESIDUE IOD B 313
19CC1SOFTWAREHIS B:21BINDING SITE FOR RESIDUE IOD B 314
20CC2SOFTWAREHOH B:398BINDING SITE FOR RESIDUE IOD B 315
21CC3SOFTWAREGLU A:164BINDING SITE FOR RESIDUE IOD A 318
22CC4SOFTWAREILE B:93BINDING SITE FOR RESIDUE IOD B 318
23CC5SOFTWARELYS B:95 , HOH B:394BINDING SITE FOR RESIDUE IOD B 319
24CC6SOFTWAREHIS A:87 , HIS A:192 , HIS A:223BINDING SITE FOR RESIDUE ZN A 319
25CC7SOFTWAREHIS B:87 , HIS B:223 , HOH B:400 , HOH B:402 , HOH B:403BINDING SITE FOR RESIDUE ZN B 320

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PM6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PM6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PM6)

(-) Exons   (0, 0)

(no "Exon" information available for 3PM6)

(-) 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:287
 aligned with ALF_COCIM | P0CJ44 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:293
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   
            ALF_COCIM     6 LKSNRALPLLTFARTHSFAIPAICVYNLEGILAIIRAAEHKRSPAMILLFPWAIQYADSLLVRTAASACRAASVPITLHLDHAQDPEIIKRAADLSRSETHEPGFDSIMVDMSHFSKEENLRLTRELVAYCNARGIATEAEPGRIEGGEDGVQDTVDLEGVLTTPEESEEFVATGINWLAPAFGNVHGNYGPRGVQLDYERLQRINEAVGERVGLVLHGADPFTKEIFEKCIERGVAKVNVNRAVNNEYVKVMREKAGSLPITRLHEEVTNAMQAAVEKIMDMIDSTGKAEFM 298
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhh.------....eeee.....hhhhhhhhhhhhhhhhhh...eeee.......................hhhhhhhhhh....ee..................hhhhhhhhhhhhh...eeee......hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pm6 A   6 LKSNRALPLLTFARTHSFAIPAICVYNLEGILAIIRAAEHKRSPAMILLFPWAIQYADSLLVRTAASACRAASVPITLHLDHAQDPEIIKRAADLS------PGFDSIMVDMSHFSKEENLRLTRELVAYCNARGIATEAEPGRIEGGEDGVQDTVDLEGVLTTPEESEEFVATGINWLAPAFGNVHGNYGPRGVQLDYERLQRINEAVGERVGLVLHGADPFTKEIFEKCIERGVAKVNVNRAVNNEYVKVMREKAGSLPITRLHEEVTNAMQAAVEKIMDMIDSTGKAEFM 298
                                    15        25        35        45        55        65        75        85        95     |   -  |    115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   
                                                                                                                         101    108                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with ALF_COCIM | P0CJ44 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:295
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
            ALF_COCIM     4 PSLKSNRALPLLTFARTHSFAIPAICVYNLEGILAIIRAAEHKRSPAMILLFPWAIQYADSLLVRTAASACRAASVPITLHLDHAQDPEIIKRAADLSRSETHEPGFDSIMVDMSHFSKEENLRLTRELVAYCNARGIATEAEPGRIEGGEDGVQDTVDLEGVLTTPEESEEFVATGINWLAPAFGNVHGNYGPRGVQLDYERLQRINEAVGERVGLVLHGADPFTKEIFEKCIERGVAKVNVNRAVNNEYVKVMREKAGSLPITRLHEEVTNAMQAAVEKIMDMIDSTGKAEFM 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---F_bP_aldolase-3pm6B01 B:7-295                                                                                                                                                                                                                                                                    --- Pfam domains (1)
           Pfam domains (2) ---F_bP_aldolase-3pm6B02 B:7-295                                                                                                                                                                                                                                                                    --- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhh...---.....eeee.....hhhhhhhhhhhhhhhhhh...eeee...-----------------...hhhhhhhhhh....ee......-----------.hhhhhhhhhhhhh...eeee......hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pm6 B   4 PSLKSNRALPLLTFARTHSFAIPAICVYNLEGILAIIRAAEHKRSPAMILLFPWAIQYADSLLVRTAASACRAASVPITLHLDHAQDPEIIKRAADLSRS---EPGFDSIMVDMSHFSKEENLRLTRELVAYCNARGIATEAEPG-----------------VLTTPEESEEFVATGINWLAPAFGN-----------LDYERLQRINEAVGERVGLVLHGADPFTKEIFEKCIERGVAKVNVNRAVNNEYVKVMREKAGSLPITRLHEEVTNAMQAAVEKIMDMIDSTGKAEFM 298
                                    13        23        33        43        53        63        73        83        93       103   |   113       123       133       143    |    -         -  |    173       183      |  -       203       213       223       233       243       253       263       273       283       293     
                                                                                                                             103 107                                      148               166                     190         202
   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 3PM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PM6)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALF_COCIM | P0CJ44)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.

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