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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOATE-BETA-ALANINE (PANTOTHENATE SYNTHETASE) FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  08 Jan 04  (Deposition) - 20 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Ligase, Rossmann Fold, Dimer, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, 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
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PANC
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
11441Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2CL5Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
11441Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2CL-1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 2 (3, 20)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2CL-1Ligand/IonCHLORIDE ION
3GOL16Ligand/IonGLYCEROL
4P6G2Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:25 , GLN A:56 , ARG A:117 , HIS A:120 , ARG A:183BINDING SITE FOR RESIDUE CL A 1301
02AC2SOFTWAREMET B:25 , GLN B:56 , ARG B:117 , HIS B:120 , ARG B:183 , HOH B:1613BINDING SITE FOR RESIDUE CL B 1302
03AC3SOFTWAREGLY A:58 , PRO A:59 , GLY A:60BINDING SITE FOR RESIDUE CL A 1303
04AC4SOFTWAREMET B:25 , HIS B:32BINDING SITE FOR RESIDUE CL B 1304
05AC5SOFTWAREMET A:25 , HIS A:32 , 144 A:1501 , HOH A:1966BINDING SITE FOR RESIDUE CL A 1305
06AC6SOFTWAREMET A:25 , GLN A:56 , VAL A:127 , GLN A:149 , CL A:1305 , HOH A:1602 , HOH A:1752 , HOH A:1966BINDING SITE FOR RESIDUE 144 A 1501
07AC7SOFTWAREARG A:2 , VAL A:4 , ALA A:13 , PHE A:45 , LYS A:194 , GLU A:231 , ARG A:233 , HOH A:1873 , HOH A:1888BINDING SITE FOR RESIDUE P6G A 1601
08AC8SOFTWAREPRO B:23 , GLN B:56 , VAL B:127 , GLN B:149 , HOH B:1441BINDING SITE FOR RESIDUE GOL B 1401
09AC9SOFTWAREGLU A:61 , ASP A:62 , ARG A:183 , ARG A:262 , ARG A:267 , HOH A:1608 , HOH A:1824BINDING SITE FOR RESIDUE GOL A 1402
10BC1SOFTWARESER A:214BINDING SITE FOR RESIDUE GOL A 1403
11BC2SOFTWARETHR A:109 , GLY A:114 , GLY A:119 , HOH A:1604 , HOH A:1610 , HOH A:1666 , GLU B:105BINDING SITE FOR RESIDUE GOL A 1404
12BC3SOFTWARETHR A:6 , GLU A:92 , HOH A:1745 , HOH A:1934 , HOH A:2036BINDING SITE FOR RESIDUE GOL A 1405
13BC4SOFTWAREALA A:99 , ARG A:101 , ALA A:115 , PRO A:118 , HOH A:1666 , HOH A:1846 , GLU B:105 , GLY B:106BINDING SITE FOR RESIDUE GOL A 1406
14BC5SOFTWAREHOH A:1733 , HIS B:241 , THR B:244 , VAL B:252 , HOH B:1497BINDING SITE FOR RESIDUE GOL B 1407
15BC6SOFTWAREGLY A:31 , HIS A:32 , LEU A:35 , PRO A:170 , THR A:171 , VAL A:172 , HOH A:1699 , HOH A:1707 , HOH A:1830 , HOH A:1871BINDING SITE FOR RESIDUE GOL A 1408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V8F)

(-) 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 1V8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V8F)

(-) Exons   (0, 0)

(no "Exon" information available for 1V8F)

(-) 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 d1v8fa_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                              SCOP domains
               CATH domains -1v8fA01 A:2-173 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1v8fA02 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...........hhhhhhhhhhhh...eee..hhhhhh.....eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeee...............eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v8f A   1 MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 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      


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 d1v8fb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                              SCOP domains
               CATH domains -1v8fB01 B:2-173 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       1v8fB02 B:174-272  [code=3.30.1300.10, no name defined]                                            ---- CATH domains
           Pfam domains (1) Pantoate_ligase-1v8fB01 B:1-274                                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) Pantoate_ligase-1v8fB02 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
                 1v8f B   1 MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP 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
   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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  1v8f
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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_THET8 | Q5SHF5: 1ufv

(-) Related Entries Specified in the PDB File

1ufv THE SAME PROTEIN MUTATION OF VAL48 TO ALA RELATED ID: TTK003000263.2 RELATED DB: TARGETDB