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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOATE-BETA-ALANINE-LIGASE IN COMPLEX WITH ATP AT LOW OCCUPANCY AT 2.1 A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  12 Aug 09  (Deposition) - 06 Oct 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Sbri, Uw, Decode, Nih, Niaid, Brucella Melitensis, Pantoate Beta Alanine Ligase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Pantothenate Biosynthesis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, D. Davies, B. Staker
Crystal Structure Of Pantoate-Beta-Alanine-Ligase In Complex With Atp At Low Occupancy At 2. 1 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B, C, D
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BMEI1593, PANC
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 29459
    Synonym: PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE- ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2UNX6Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:28 , MET A:30 , HIS A:34 , HIS A:37 , LEU A:40 , GLN A:61 , VAL A:131 , PHE A:146 , GLY A:147 , LYS A:149 , ASP A:150 , GLN A:153 , THR A:175 , VAL A:176 , CYS A:184 , HOH A:439 , HOH A:472 , HOH A:691BINDING SITE FOR RESIDUE ATP A 300
2AC2SOFTWAREPRO C:28 , THR C:29 , MET C:30 , HIS C:34 , HIS C:37 , LEU C:40 , GLN C:61 , VAL C:132 , PHE C:146 , GLY C:147 , ASP C:150 , GLN C:153 , THR C:175 , VAL C:176 , CYS C:184 , HOH C:317 , HOH C:393 , HOH C:528 , HOH C:732BINDING SITE FOR RESIDUE ATP C 300
3AC3SOFTWAREPRO D:28 , THR D:29 , MET D:30 , GLY D:31 , HIS D:34 , HIS D:37 , LEU D:40 , GLN D:61 , PHE D:146 , GLY D:147 , ASP D:150 , GLN D:153 , THR D:175 , VAL D:176 , CYS D:184 , HOH D:483 , HOH D:733BINDING SITE FOR RESIDUE ATP D 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3INN)

(-) 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:283
 aligned with PANC_BRUME | Q8YFC9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:283
                             1                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
           PANC_BRUME     - -MQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQMEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGH 282
               SCOP domains d3inna_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --3innA01 A:2-177 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                           3innA02 A:178-278  [code=3.30.1300.10, no name defined]                                              ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...........hhhhhhhhhhhh...eee..hhhhhh......eeehhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeeee...............eeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inn A   0 SMQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQIEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGH 282
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with PANC_BRUME | Q8YFC9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:287
                             1                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
           PANC_BRUME     - -MQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQMEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHAAPQ 286
               SCOP domains d3innb_ B: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --3innB01 B:2-177 Tyrosyl-Transfer RNA Synthetase , subunit E, dom         ain 1                                                                                                  3innB02 B:178-278  [code=3.30.1300.10, no name defined]                                              -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...---------hhhhhhhhhhh...eee..hhhhhh......eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee...............eeeeeeeee..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inn B   0 SMQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGAN---------LERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQIEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHAAPQ 286
                                     9        19        29        39        49        59     |   -     |  79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
                                                                                            65        75                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:284
 aligned with PANC_BRUME | Q8YFC9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:284
                             1                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
           PANC_BRUME     - -MQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQMEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHA 283
               SCOP domains d3innc_ C: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --3innC01 C:2-177 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                           3innC02 C:178-278  [code=3.30.1300.10, no name defined]                                              ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...........hhhhhhhhhhhh...eee..hhhhhh......eeehhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee...............eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inn C   0 SMQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQIEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHA 283
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    


Chain D from PDB  Type:PROTEIN  Length:277
 aligned with PANC_BRUME | Q8YFC9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:287
                             1                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
           PANC_BRUME     - -MQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGANEDLGRYPRDLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQMEGEARPGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHAAPQ 286
               SCOP domains d3innd_ D: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --3innD01 D:2-177 Tyrosyl-Transfer RNA Synthetase , subunit E, dom        ain 1                                                                                                   3innD02 D:178-278  [code=3.30.1300.10, no name defined]                                              -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..........--------hhhhhhhhhhhh...eee..hhhhhh......eeehhhhhhhhhhh--...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee...............eeeeeeeee..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inn D   0 SMQIIHTIEELRQALAPARQQGKKIGFVPTMGYLHKGHLELVRRARVENDVTLVSIFVNPLQFGAN--------DLERDAGLLHDAQVDYLFAPTVSDMYPRPMQTVVDVPPLGNQIEGE--PGHFAGVATVVSKLFNIVGPDAAYFGEKDFQQLVIIRRMVDDMAIPVRIVGVETVREDDGLACSSRNVYLTPEQRRAAIIVPQALDEADRLYRSGMDDPDALEAAIRTFIGRQPLAVPEVIAIRDPETLERLPALQGRPILVALFVRVGATRLLDNRVIGHAAPQ 286
                                     9        19        29        39        49        59     |   -    |   79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
                                                                                            65       74                                          119  |                                                                                                                                                                    
                                                                                                                                                    122
   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, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3INN)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PANC_BRUME | Q8YFC9)
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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