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(-) Description

Title :  AZOTOBACTER VINELANDII MANNURONAN C-5 EPIMERASE ALGE4 A-MODULE COMPLEXED WITH MANNURONAN TRISACCHARIDE
 
Authors :  H. J. Rozeboom, T. M. Bjerkan, K. H. Kalk, H. Ertesvag, S. Holtan, F. L. Aa S. Valla, B. W. Dijkstra
Date :  16 May 07  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,D#
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Beta-Helix, Epimerase, Mannuronic Acid, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Rozeboom, T. M. Bjerkan, K. H. Kalk, H. Ertesvag, S. Holtan, F. L. Aachmann, S. Valla, B. W. Dijkstra
Structural And Mutational Characterization Of The Catalytic A-Module Of The Mannuronan C-5-Epimerase Alge4 From Azotobacter Vinelandii.
J. Biol. Chem. V. 283 23819 2008
PubMed-ID: 18574239  |  Reference-DOI: 10.1074/JBC.M804119200

(-) Compounds

Molecule 1 - POLY(BETA-D-MANNURONATE) C5 EPIMERASE 4
    Chains: A, B
    EC Number: 5.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTB26 DERIVATIVE OF PTYB5 (NEB)
    Expression System Strain: ER2566
    Expression System Vector Type: PLASMID
    Fragment: A-MODULE
    Gene: ALGE4
    Organism Scientific: AZOTOBACTER VINELANDII
    Synonym: MANNURONAN EPIMERASE 4

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD#
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2MAV3Ligand/IonALPHA-D-MANNOPYRANURONIC ACID
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAV-1Ligand/IonALPHA-D-MANNOPYRANURONIC ACID
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAV-1Ligand/IonALPHA-D-MANNOPYRANURONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:149 , ARG B:195 , ASN B:199 , GLN B:225 , GLY B:227 , LEU B:228BINDING SITE FOR RESIDUE MAV D 601
2AC2SOFTWAREARG B:195 , HIS B:196 , GLN B:225 , LEU B:228 , LYS B:255BINDING SITE FOR RESIDUE MAV D 602
3AC3SOFTWARELYS B:255 , TYR B:278BINDING SITE FOR RESIDUE MAV D 603
4AC4SOFTWARESER B:91 , ALA B:92 , GLU B:95 , THR B:97 , GLY B:124 , ASP B:133BINDING SITE FOR RESIDUE CA B 378
5AC5SOFTWARESER A:91 , ALA A:92 , GLU A:95 , THR A:97 , ASP A:133BINDING SITE FOR RESIDUE CA A 378
6AC6SOFTWAREARG B:111 , THR B:114BINDING SITE FOR RESIDUE CA B 379
7AC7SOFTWAREGLU A:229 , ASP A:292 , SER A:331 , GLY A:332BINDING SITE FOR RESIDUE CA A 380
8AC8SOFTWARETHR B:310BINDING SITE FOR RESIDUE CA B 381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PYH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:155 -Gln A:156
2Glu B:155 -Gln B:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PYH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PYH)

(-) Exons   (0, 0)

(no "Exon" information available for 2PYH)

(-) 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:376
 aligned with ALGE4_AZOVI | Q44493 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:376
                                    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       280       290       300       310       320       330       340       350       360       370      
          ALGE4_AZOVI     1 MDYNVKDFGALGDGVSDDRASIQAAIDAAYAAGGGTVYLPAGEYRVSAAGEPGDGCLMLKDGVYLAGAGMGETVIKLIDGSDQKITGMVRSAYGEETSNFGMRDLTLDGNRDNTSGKVDGWFNGYIPGGDGADRDVTIERVEVREMSGYGFDPHEQTINLTIRDSVAHDNGLDGFVADYLVDSVFENNVAYANDRHGFNVVTSTHDFVMTNNVAYGNGSSGLVVQRGLEDLALPSNILIDGGAYYDNAREGVLLKMTSDITLQNADIHGNGSSGVRVYGAQDVQILDNQIHDNAQAAAVPEVLLQSFDDTAGASGTYYTTLNTRIEGNTISGSANSTYGIQERNDGTDYSSLIDNDIAGVQQPIQLYGPHSTVSGE 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhh...eeeeehhhhhhhhhhhhhhh..eeeee..eeeee....hhhhh.eee...eeeee.....eeeee...........eee......eeeeeeeeeee............eee.........eeeeeeeeeeee......eee...eeeeeee..eee......eeee.eeeeeee..eee......eeee...eeeeeeeeeee......eeee.........eeeeeeeeeee......eeeeeeeeeeee..eee......eeeeeeeeeeee..eee..........eeee.ee........ee..eeeeee..eee......eeeee.....eeeeee..eee...eeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyh A   1 MDYNVKDFGALGDGVSDDRASIQAAIDAAYAAGGGTVYLPAGEYRVSAAGEPGDGCLMLKDGVYLAGAGMGETVIKLIDGSDQKITGMVRSAYGEETSNFGMRDLTLDGNRDNTSGKVDGWFNGYIPGGDGADRDVTIERVEVREMSGYGFDPHEQTINLTIRDSVAHDNGLDGFVADYLVDSVFENNVAYANDRHGFNVVTSTHDFVMTNNVAYGNGSSGLVVQRGLEDLALPSNILIDGGAYYDNAREGVLLKMTSDITLQNADIHGNGSSGVRVYGAQDVQILDNQIHDNAQAAAVPEVLLQSFDDTAGASGTYYTTLNTRIEGNTISGSANSTYGIQERNDGTDYSSLIDNDIAGVQQPIQLYGPHSTVSGE 376
                                    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       280       290       300       310       320       330       340       350       360       370      


Chain B from PDB  Type:PROTEIN  Length:377
 aligned with ALGE4_AZOVI | Q44493 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:377
                                    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       280       290       300       310       320       330       340       350       360       370       
          ALGE4_AZOVI     1 MDYNVKDFGALGDGVSDDRASIQAAIDAAYAAGGGTVYLPAGEYRVSAAGEPGDGCLMLKDGVYLAGAGMGETVIKLIDGSDQKITGMVRSAYGEETSNFGMRDLTLDGNRDNTSGKVDGWFNGYIPGGDGADRDVTIERVEVREMSGYGFDPHEQTINLTIRDSVAHDNGLDGFVADYLVDSVFENNVAYANDRHGFNVVTSTHDFVMTNNVAYGNGSSGLVVQRGLEDLALPSNILIDGGAYYDNAREGVLLKMTSDITLQNADIHGNGSSGVRVYGAQDVQILDNQIHDNAQAAAVPEVLLQSFDDTAGASGTYYTTLNTRIEGNTISGSANSTYGIQERNDGTDYSSLIDNDIAGVQQPIQLYGPHSTVSGEP 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Pectate_lyase_3-2pyhB01 B:3-299                                                                                                                                                                                                                                                                          ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --Pectate_lyase_3-2pyhB02 B:3-299                                                                                                                                                                                                                                                                          ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..ee.hhhh...eeeeehhhhhhhhhhhhhhh..eeee...eeeee....hhhhh.eee...eeee......eeeee...........eee......eeeeeeeeeee.hhhhh......eee.........eeeeeeeeeeee......eee...eeeeeee..eee......eeee.eeeeeee..eee......eeee...eeeeee..eee......eeee.........eeeeee..eee......eeee..eeeeee..eee......eeee.....eee..eee..........eeee.ee........ee....eeee..eee......eeeee.......eeee..eee...eeee......eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyh B   1 MDYNVKDFGALGDGVSDDRASIQAAIDAAYAAGGGTVYLPAGEYRVSAAGEPGDGCLMLKDGVYLAGAGMGETVIKLIDGSDQKITGMVRSAYGEETSNFGMRDLTLDGNRDNTSGKVDGWFNGYIPGGDGADRDVTIERVEVREMSGYGFDPHEQTINLTIRDSVAHDNGLDGFVADYLVDSVFENNVAYANDRHGFNVVTSTHDFVMTNNVAYGNGSSGLVVQRGLEDLALPSNILIDGGAYYDNAREGVLLKMTSDITLQNADIHGNGSSGVRVYGAQDVQILDNQIHDNAQAAAVPEVLLQSFDDTAGASGTYYTTLNTRIEGNTISGSANSTYGIQERNDGTDYSSLIDNDIAGVQQPIQLYGPHSTVSGEP 377
                                    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       280       290       300       310       320       330       340       350       360       370
   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 2PYH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PYH)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ALGE4_AZOVI | Q44493)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0042121    alginic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALGE4_AZOVI | Q44493: 2agm 2pyg

(-) Related Entries Specified in the PDB File

2pyg AZOTOBACTER VINELANDII MANNURONAN C-5 EPIMERASE ALGE4 A- MODULE