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(-) Description

Title :  CRYSTAL STRUCTURE OF RUMINOCOCCUS ALBUS BETA-(1,4)-MANNOOLIGOSACCHARIDE PHOSPHORYLASE (RAMP2) IN COMPLEXES WITH PHOSPHATE AND BETA-(1,4)-MANNOBIOSE
 
Authors :  Y. Ye, W. Saburi, K. Kato, M. Yao
Date :  13 Aug 15  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Glycoside Hydrolase Family 130, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Ye, W. Saburi, R. Odaka, K. Kato, N. Sakurai, K. Komoda, M. Nishimoto M. Kitaoka, H. Mori, M. Yao
Structural Insights Into The Difference In Substrate Recognition Of Two Mannoside Phosphorylases From Two Gh130 Subfamilies.
Febs Lett. V. 590 828 2016
PubMed-ID: 26913570  |  Reference-DOI: 10.1002/1873-3468.12105

(-) Compounds

Molecule 1 - BETA-1,4-MANNOOLIGOSACCHARIDE PHOSPHORYLASE
    Chains: A, B, C, D, E, F
    EC Number: 2.4.1.319
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-335
    Gene: RUMAL_0099
    Organism Scientific: RUMINOCOCCUS ALBUS (STRAIN ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7)
    Organism Taxid: 697329
    Strain: ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7
    Synonym: RAMP2

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1BMA12Ligand/IonBETA-D-MANNOSE
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:162 , ASN A:163 , ARG A:180 , LYS A:220 , HIS A:239 , TYR A:250 , BMA A:403binding site for residue PO4 A 401
02AC2SOFTWAREARG B:162 , ASN B:163 , ARG B:180 , LYS B:220 , HIS B:239 , TYR B:250 , BMA B:403binding site for residue PO4 B 401
03AC3SOFTWAREARG C:162 , ASN C:163 , ARG C:180 , LYS C:220 , HIS C:239 , TYR C:250 , BMA C:403binding site for residue PO4 C 401
04AC4SOFTWAREARG D:162 , ASN D:163 , ARG D:180 , LYS D:220 , HIS D:239 , TYR D:250 , BMA D:403binding site for residue PO4 D 401
05AC5SOFTWAREARG E:162 , ASN E:163 , ARG E:180 , LYS E:220 , HIS E:239 , TYR E:250 , BMA E:403binding site for residue PO4 E 401
06AC6SOFTWAREARG F:162 , ASN F:163 , ARG F:180 , LYS F:220 , HIS F:239 , TYR F:250 , BMA F:403binding site for residue PO4 F 401
07AC7SOFTWAREASN A:49 , ARG A:67 , TYR A:114 , ASP A:115 , ARG A:162 , HIS A:186 , TYR A:250 , PHE A:291 , ASP A:312 , PO4 A:401 , HOH A:501 , HOH A:511 , HOH A:513 , HOH A:577 , CYS C:245binding site for Poly-Saccharide residues BMA A 402 through BMA A 403
08AC8SOFTWARECYS A:245 , ASN B:49 , ARG B:67 , TYR B:114 , ASP B:115 , ARG B:162 , HIS B:186 , TYR B:250 , PHE B:291 , ASP B:312 , PO4 B:401 , HOH B:517 , HOH B:558 , HOH B:580 , HOH B:638 , HOH B:646 , HOH B:666binding site for Poly-Saccharide residues BMA B 402 through BMA B 403
09AC9SOFTWARECYS B:245 , HOH B:611 , ASN C:49 , ARG C:67 , TYR C:114 , ASP C:115 , ARG C:162 , GLY C:185 , HIS C:186 , TYR C:250 , ASP C:312 , PO4 C:401 , HOH C:543 , HOH C:601binding site for Poly-Saccharide residues BMA C 402 through BMA C 403
10AD1SOFTWAREASN D:49 , ARG D:67 , TYR D:114 , ASP D:115 , ARG D:162 , HIS D:186 , TYR D:250 , PHE D:291 , ASP D:312 , PO4 D:401 , HOH D:536 , HOH D:571 , HOH D:575 , HOH D:596 , CYS E:245 , HOH E:625binding site for Poly-Saccharide residues BMA D 402 through BMA D 403
11AD2SOFTWAREASN E:49 , ARG E:67 , TYR E:114 , ASP E:115 , ARG E:162 , HIS E:186 , TYR E:250 , VAL E:289 , ASP E:312 , PO4 E:401 , HOH E:511 , HOH E:532 , HOH E:545 , HOH E:667 , CYS F:245binding site for Poly-Saccharide residues BMA E 402 through BMA E 403
12AD3SOFTWARECYS D:245 , HOH D:635 , ASN F:49 , ARG F:67 , TYR F:114 , ASP F:115 , ARG F:162 , HIS F:186 , TYR F:250 , PHE F:291 , ASP F:312 , PO4 F:401 , HOH F:516 , HOH F:581 , HOH F:656 , HOH F:694binding site for Poly-Saccharide residues BMA F 402 through BMA F 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AYE)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Asn A:33 -Pro A:34
2Pro A:159 -Phe A:160
3Asn B:33 -Pro B:34
4Pro B:159 -Phe B:160
5Asn C:33 -Pro C:34
6Pro C:159 -Phe C:160
7Asn D:33 -Pro D:34
8Pro D:159 -Phe D:160
9Asn E:33 -Pro E:34
10Pro E:159 -Phe E:160
11Asn F:33 -Pro F:34
12Pro F:159 -Phe F:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AYE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AYE)

(-) Exons   (0, 0)

(no "Exon" information available for 5AYE)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeee....eeeeeeee.....eee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye A   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee.....eee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee............ee........eeeee............eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye B   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeee....eeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye C   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain D from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee.....eee.......ee.hhhhh.......eeeeeeeee..eeeeeeeee....eeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye D   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain E from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee.....eee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye E   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain F from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aye F   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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
   Legend:   → Mismatch (orange background)
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  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 5AYE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AYE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AYE)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  5aye
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        MOSP_RUMA7 | E6UBR9: 5ayd

(-) Related Entries Specified in the PDB File

5ay9 5ayc 5ayd