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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, S. Kuramitsu, S. Yokoyama, M. Miyano, T. H. Tahirov, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Jun 03  (Deposition) - 24 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Structural Genomics, Dimer, Domains, Rossmann Fold, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, S. Kuramitsu, S. Yokoyama, M. Miyano, T. H. Tahirov
Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PANTOATE-BETA-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PANC
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Other Details: MUTATION OF VAL 48 TO ALA
    Synonym: PANTOTHENATE SYNTHETASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 30)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL10Ligand/IonGLYCEROL
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:56 , ARG A:117 , HIS A:120 , ARG A:183BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWAREHIS A:29 , SER A:182 , GOL A:1300BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWAREMSE B:25 , GLN B:56 , ARG B:117 , ARG B:183BINDING SITE FOR RESIDUE CL B 1003
4AC4SOFTWAREPRO A:23 , THR A:24 , MSE A:25 , HIS A:32 , LEU A:35 , CL A:1002 , GOL A:1400 , HOH A:1423 , HOH A:1431 , HOH A:1562BINDING SITE FOR RESIDUE GOL A 1300
5AC5SOFTWAREGLN A:56 , VAL A:127 , GLN A:149 , GOL A:1300 , HOH A:1401 , HOH A:1567BINDING SITE FOR RESIDUE GOL A 1400
6AC6SOFTWAREGLN B:56 , VAL B:127 , GLN B:149 , HOH B:1032BINDING SITE FOR RESIDUE GOL B 500
7AC7SOFTWAREGLU A:61 , ASP A:62 , ARG A:117 , ARG A:183 , ARG A:267 , HOH A:1409BINDING SITE FOR RESIDUE GOL A 600
8AC8SOFTWARELEU A:55 , TYR A:94 , ARG A:101 , PRO A:118 , HOH A:1559 , HOH A:1653BINDING SITE FOR RESIDUE GOL A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UFV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:275 -Pro A:276
2Tyr B:275 -Pro B:276

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UFV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UFV)

(-) Exons   (0, 0)

(no "Exon" information available for 1UFV)

(-) 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:276
 aligned with PANC_THET8 | Q5SHF5 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
           PANC_THET8     1 MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 276
               SCOP domains d1ufva_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                              SCOP domains
               CATH domains -1ufvA01 A:2-173 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1ufvA02 A:174-272  [code=3.30.1300.10, no name defined]                                            ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.hhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...........hhhhhhhhhhhhh..eee..hhhhhh.....eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeee...............eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ufv A   1 mRTVSTVAELRAALPREGVGFVPTmGYLHRGHLALVERARRENPFVVASVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEmYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRmVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAmREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 276
                            |       10        20    |   30        40        50        60        70        80        90  |    100       110       120       130       140       150     | 160       170       180       190       200    |  210       220       230       240       250       260       270      
                            |                      25-MSE                                                              93-MSE                                                        156-MSE                                          205-MSE                                                                   
                            1-MSE                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with PANC_THET8 | Q5SHF5 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
           PANC_THET8     1 MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 276
               SCOP domains d1ufvb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                              SCOP domains
               CATH domains -1ufvB01 B:2-173 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1ufvB02 B:174-272  [code=3.30.1300.10, no name defined]                                            ---- CATH domains
           Pfam domains (1) Pantoate_ligase-1ufvB01 B:1-274                                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) Pantoate_ligase-1ufvB02 B:1-274                                                                                                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author .eee.hhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...........hhhhhhhhhhhhh..eee..hhhhhh.....eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeee...............eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ufv B   1 mRTVSTVAELRAALPREGVGFVPTmGYLHRGHLALVERARRENPFVVASVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEmYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRmVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAmREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 276
                            |       10        20    |   30        40        50        60        70        80        90  |    100       110       120       130       140       150     | 160       170       180       190       200    |  210       220       230       240       250       260       270      
                            1-MSE                  25-MSE                                                              93-MSE                                                        156-MSE                                          205-MSE
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PANC_THET8 | Q5SHF5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004592    pantoate-beta-alanine ligase activity    Catalysis of the reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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